Toxin expression data were collected from 39 publications (Supplementary table 1). The selection criteria for toxins and taxa are the same as in (Barua and Mikheyev 2019). We scaled gene expression levels by the average within-species variance allowing us to standardize the measurements and carry out comparisons across toxins. This scaled dataset was used in all subsequent analysis. We used a previously described time-calibrated phylogeny of squamates based on two large datasets comprising of 44 nuclear genes for 161 squamates, and a dataset of 12 genes from 4161 squamate species, both these datasets represented families and subfamilies (Wiens et al. 2012; Pyron et al. 2013; Zheng and Wiens 2016; Barua and Mikheyev 2019).
library(tidyverse)
library(ggplot2)
library(reshape2)
library(geiger)
library(spptest)
library(BAMMtools)
library(ape)
library(phytools)
library(coda)
library(kableExtra)
library(OUwie)
tree <- read.newick("./Final_tree.tre")
plotTree(tree)
Check if tree is ultrametric
is.ultrametric(tree)
## [1] TRUE
Toxin expression data was collected from 39 publications (online supp). Out of the 25 reported toxin families we selected only 10 as they were the most ubiquitous toxins amongst all snakes. We restricted our dataset to include components that are found in at least 50% of snakes and eliminated low-abundance toxin families (Supplementary Fig 34 & 35). Incidentally, this cutoff also eliminated many low-abundance toxin families (on average less than 1% of the venom). The abundance of these toxins would be more difficult to estimate, as they are closer to the signal to noise to threshold of gene expression experiments. Overall 10 out of 25 toxin families we retained. Toxins levels were recorded as per publication. Toxin values reported as absolute FPKM values, were converted to a percentages of total toxin transcript expression.
dat<-read.csv("./data/scaleddata/vPhen_data.csv", header = T)
Supplementary Table 1: Gene expression values and references| species | TFTx | BPP.CNP | CRISP | CTL | GF | KSPI | LAAO | ePLA2 | vPLA2 | SVMP | SVSP | Total | cm | Family | Author | Tech | Ref |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Agkistrodon_piscivorus | 0.00000 | 0.04570 | 0.00000 | 0.06080 | 0.00000 | 0.00000 | 0.00000 | 0.00000 | 0.38960 | 0.34900 | 0.08300 | 0.92810 | 127.0 | Viperidae | Aronow (2018) | Illumina | https://search.proquest.com/openview/2997dede40d17e51e7dabfd03d9762df/1?pq-origsite=gscholar&cbl=18750&diss=y |
| Atropoides_picadoi | 0.00400 | 0.16400 | 0.02600 | 0.04800 | 0.00600 | 0.00010 | 0.03100 | 0.00000 | 0.02300 | 0.56100 | 0.10900 | 0.97210 | 120.2 | Viperidae | Durban et al. (2011) | Roche GS FLX | https://doi.org/10.1186/1471-2164-12-259 |
| Bitis_gabonica | 0.00000 | 0.01813 | 0.00000 | 0.07591 | 0.03626 | 0.09064 | 0.05665 | 0.00000 | 0.05665 | 0.37729 | 0.14729 | 0.85882 | 120.0 | Viperidae | Francischetti et al. (2004) | Beckman Coulter | https://doi.org/10.1016/j.gene.2004.03.024 |
| Boiga_irregularis | 0.67475 | 0.01400 | 0.03835 | 0.02271 | 0.00025 | 0.00100 | 0.00000 | 0.00040 | 0.00000 | 0.24854 | 0.00000 | 1.00000 | 270.0 | Colubridae | McGivern et al. (2014) | Illumina | https://doi.org/10.1186/1471-2164-15-1061 |
| Bothriechis_lateralis | 0.01600 | 0.23600 | 0.03200 | 0.03100 | 0.01800 | 0.00020 | 0.03400 | 0.00000 | 0.03000 | 0.44900 | 0.10400 | 0.95020 | 90.0 | Viperidae | Durban et al. (2011) | Roche GS FLX | https://doi.org/10.1186/1471-2164-12-259 |
| Bothriechis_schlegelii | 0.03600 | 0.15300 | 0.03600 | 0.00200 | 0.04900 | 0.00120 | 0.03200 | 0.00000 | 0.09200 | 0.26300 | 0.20500 | 0.86920 | 55.0 | Viperidae | Durban et al. (2011) | Roche GS FLX | https://doi.org/10.1186/1471-2164-12-259 |
| Bothrops_alternatus | 0.00000 | 0.11800 | 0.02200 | 0.16500 | 0.02500 | 0.00000 | 0.01800 | 0.00000 | 0.01400 | 0.58500 | 0.05100 | 0.99800 | 100.0 | Viperidae | Pereira de Paula et al. (2014) | MegaBACE (GE) | https://doi.org/10.1016/j.cbd.2014.09.001 |
| Bothrops_asper | 0.00800 | 0.15000 | 0.00800 | 0.01000 | 0.00000 | 0.00030 | 0.04200 | 0.00000 | 0.17800 | 0.41600 | 0.13400 | 0.94630 | 150.0 | Viperidae | Durban et al. (2011) | Roche GS FLX | https://doi.org/10.1186/1471-2164-12-259 |
| Bothrops_atrox | 0.00000 | 0.07100 | 0.00500 | 0.04800 | 0.01000 | 0.00000 | 0.01400 | 0.00000 | 0.14600 | 0.61600 | 0.08200 | 0.99200 | 100.0 | Viperidae | Neiva et al. (2009) | MegaBACE (GE) | https://doi.org/10.1016/j.toxicon.2009.01.006 |
| Bothrops_colombiensis | 0.00000 | 0.01000 | 0.02000 | 0.04000 | 0.02000 | 0.00000 | 0.02000 | 0.00000 | 0.30000 | 0.37000 | 0.12000 | 0.90000 | 100.0 | Viperidae | Suntravat et al. (2016) | ABI 3730 | https://doi.org/10.1186/s12867-016-0059-7 |
| Bothrops_insularis | 0.00000 | 0.15800 | 0.01500 | 0.14200 | 0.05100 | 0.00000 | 0.03500 | 0.00000 | 0.05400 | 0.43200 | 0.11200 | 0.99900 | 150.0 | Viperidae | Valente et al. (2009) | ABI 3100 | https://doi.org/10.1016/j.jprot.2009.01.001 |
| Bothrops_jararaca | 0.00000 | 0.04250 | 0.00400 | 0.13650 | 0.02900 | 0.00200 | 0.04050 | 0.00000 | 0.03600 | 0.43600 | 0.26100 | 0.98750 | 160.0 | Viperidae | Goncalves-Machado et al. (2016) | Roche GS FLX | https://doi.org/10.1016/j.jprot.2015.04.029 |
| Bothrops_jararacussu | 0.00000 | 0.01695 | 0.03390 | 0.08475 | 0.00000 | 0.00000 | 0.01695 | 0.00000 | 0.56290 | 0.25820 | 0.01695 | 0.99060 | 70.0 | Viperidae | Kashima et al. (2004) | ABI 3100 | https://doi.org/10.1016/j.biochi.2004.02.002 |
| Bothrops_moojeni | 0.00060 | 0.00950 | 0.00570 | 0.02670 | 0.00000 | 0.00440 | 0.01270 | 0.00000 | 0.09020 | 0.46630 | 0.26180 | 0.87790 | 130.0 | Viperidae | Amorim et al. (2017) | Illumina | https://doi.org/10.1016/j.toxicon.2017.10.025 |
| Bothrops_neuwiedi | 0.00000 | 0.17400 | 0.00700 | 0.08600 | 0.00360 | 0.00000 | 0.02900 | 0.00000 | 0.26400 | 0.36000 | 0.05300 | 0.97660 | 65.0 | Viperidae | Rodigues et al. (2012) | MegaBACE (GE) | https://doi.org/10.1016/j.jprot.2012.03.028 |
| Bungarus_flaviceps | 0.39290 | 0.00000 | 0.00440 | 0.00440 | 0.00000 | 0.24060 | 0.00000 | 0.35320 | 0.00000 | 0.00000 | 0.00000 | 0.99550 | 185.0 | Elapidae | Siang et al. (2010) | ABI PRISM | https://dx.doi.org/10.1186/1471-2199-11-24 |
| Bungarus_multicinctus | 0.64700 | 0.00000 | 0.00700 | 0.03800 | 0.00200 | 0.10600 | 0.00100 | 0.17400 | 0.00000 | 0.00000 | 0.00100 | 0.97600 | 125.0 | Elapidae | Jiang et al. (2011) | ABI 3100 | https://doi.org/10.1186/1471-2164-12-1 |
| Cerrophidion_godmani | 0.00600 | 0.08300 | 0.02600 | 0.00200 | 0.00600 | 0.00000 | 0.05500 | 0.00000 | 0.07900 | 0.42200 | 0.28100 | 0.96000 | 55.0 | Viperidae | Durban et al. (2011) | Roche GS FLX | https://doi.org/10.1186/1471-2164-12-259 |
| Crotalus_adamanteus | 0.00000 | 0.00726 | 0.01317 | 0.22155 | 0.00023 | 0.00054 | 0.05309 | 0.00000 | 0.07810 | 0.24410 | 0.19979 | 0.81783 | 244.0 | Viperidae | Rokyta et al. (2012) | Illumina | https://doi.org/10.1186/1471-2164-13-312 |
| Crotalus_durissus | 0.00000 | 0.00000 | 0.00000 | 0.00000 | 0.04000 | 0.00000 | 0.00000 | 0.00000 | 0.88000 | 0.03000 | 0.02500 | 0.97500 | 150.0 | Viperidae | Boldrini-Franca et al. (2009) | MegaBACE (GE) | https://doi.org/10.1016/j.biochi.2009.02.001 |
| Crotalus_horridus | 0.00000 | 0.12519 | 0.00775 | 0.00213 | 0.02285 | 0.00119 | 0.01106 | 0.00000 | 0.22772 | 0.00111 | 0.58229 | 0.98129 | 121.0 | Viperidae | Rokyta et al. (2013) | Illumina | https://doi.org/10.1186/1471-2164-14-394 |
| Crotalus_scutulatus | 0.00000 | 0.20121 | 0.00481 | 0.16943 | 0.02000 | 0.00021 | 0.00925 | 0.00000 | 0.18171 | 0.14363 | 0.11692 | 0.84717 | 137.3 | Viperidae | Strickland et al. (2018) | Illumina | https://dx.doi.org/10.3390/toxins10040135 |
| Crotalus_simus | 0.12700 | 0.13400 | 0.00000 | 0.02400 | 0.00000 | 0.00150 | 0.03800 | 0.00000 | 0.12100 | 0.06500 | 0.28100 | 0.79150 | 150.0 | Viperidae | Durban et al. (2011) | Roche GS FLX | https://doi.org/10.1186/1471-2164-12-259 |
| Dispholidus_typus | 0.06200 | 0.00000 | 0.05400 | 0.00400 | 0.00100 | 0.00150 | 0.00000 | 0.07600 | 0.00000 | 0.74640 | 0.05500 | 0.99990 | 135.0 | Colubridae | Pla et al. (2017) | Illumina | https://doi.org/10.1016/j.bbagen.2017.01.020 |
| Drysdalia_coronoides | 0.86000 | 0.00000 | 0.02800 | 0.00000 | 0.01400 | 0.00000 | 0.00000 | 0.00240 | 0.00000 | 0.00000 | 0.09200 | 0.99640 | 40.0 | Elapidae | Chatrath et al. (2011) | ABI PRISM | https://dx.doi.org/10.1021/pr1008916 |
| Echis_carinatus | 0.00000 | 0.00000 | 0.01934 | 0.17602 | 0.00580 | 0.00193 | 0.01161 | 0.00000 | 0.08317 | 0.64603 | 0.04836 | 0.99226 | 60.0 | Viperidae | Casewell et al. (2009) | ABI 3730 | https://doi.org/10.1186/1471-2164-10-564 |
| Echis_coloratus | 0.00000 | 0.00000 | 0.05426 | 0.10543 | 0.00620 | 0.00000 | 0.04031 | 0.00000 | 0.05426 | 0.68527 | 0.04496 | 0.99069 | 62.7 | Viperidae | Casewell et al. (2009) | ABI 3730 | https://doi.org/10.1186/1471-2164-10-564 |
| Echis_ocellatus | 0.00000 | 0.00000 | 0.00297 | 0.10979 | 0.02671 | 0.00193 | 0.01187 | 0.00000 | 0.08605 | 0.73591 | 0.02374 | 0.99897 | 40.0 | Viperidae | Casewell et al. (2009) | ABI 3730 | https://doi.org/10.1186/1471-2164-10-564 |
| Echis_pyramidum | 0.00000 | 0.00000 | 0.00000 | 0.24011 | 0.00582 | 0.00000 | 0.02639 | 0.00000 | 0.20580 | 0.50000 | 0.01979 | 0.99791 | 65.0 | Viperidae | Casewell et al. (2009) | ABI 3730 | https://doi.org/10.1186/1471-2164-10-564 |
| Gloydius_intermedius | 0.00000 | 0.04900 | 0.04900 | 0.04900 | 0.14600 | 0.00000 | 0.02400 | 0.00000 | 0.12200 | 0.17000 | 0.22000 | 0.82900 | 53.3 | Viperidae | Yang et al. (2015) | MegaBACE (GE) | https://doi.org/10.1016/j.toxicon.2015.08.010 |
| Hypsiglena_torquata | 0.00070 | 0.07359 | 0.16684 | 0.06176 | 0.00012 | 0.00056 | 0.00000 | 0.00000 | 0.00000 | 0.68666 | 0.00000 | 0.99023 | 48.0 | Colubridae | McGivern et al. (2014) | Illumina | https://doi.org/10.1186/1471-2164-15-1061 |
| Lachesis_muta | 0.01600 | 0.73200 | 0.00000 | 0.05800 | 0.00300 | 0.00000 | 0.03700 | 0.00000 | 0.04700 | 0.05900 | 0.03500 | 0.98700 | 225.0 | Viperidae | Lnacio et al. (2007) | ABI 3100 | https://doi.org/10.1534/genetics.106.056515 |
| Micrurus_altirostris | 0.86400 | 0.00000 | 0.00000 | 0.01300 | 0.00000 | 0.03800 | 0.00000 | 0.04900 | 0.00000 | 0.00600 | 0.00000 | 0.97000 | 64.0 | Elapidae | Correa-Netto et al. (2011) | ABI 3100 | https://doi.org/10.1016/j.jprot.2011.04.003 |
| Micrurus_corallinus | 0.20300 | 0.29530 | 0.00000 | 0.06700 | 0.01830 | 0.00150 | 0.00840 | 0.37680 | 0.00000 | 0.02100 | 0.00100 | 0.99230 | 72.5 | Elapidae | Aird et al. (2017) | Illumina | https://dx.doi.org/10.3390/toxins9060187 |
| Micrurus_fulvius | 0.25160 | 0.00000 | 0.00000 | 0.00799 | 0.01600 | 0.02154 | 0.00880 | 0.64947 | 0.00000 | 0.02947 | 0.00000 | 0.98487 | 55.0 | Elapidae | Margres et al. (2013) | Illumina | https://doi.org/10.1186/1471-2164-14-531 |
| Micrurus_lemniscatus | 0.67220 | 0.00200 | 0.00240 | 0.00480 | 0.01420 | 0.07150 | 0.00730 | 0.17200 | 0.00000 | 0.01120 | 0.00100 | 0.95860 | 120.0 | Elapidae | Aird et al. (2017) | Illumina | https://dx.doi.org/10.3390/toxins9060187 |
| Micrurus_spixii | 0.62640 | 0.00000 | 0.00000 | 0.00000 | 0.00000 | 0.00000 | 0.00000 | 0.36390 | 0.00000 | 0.00000 | 0.00000 | 0.99030 | 75.0 | Elapidae | Aird et al. (2017) | Illumina | https://dx.doi.org/10.3390/toxins9060187 |
| Micrurus_surinamensis | 0.60240 | 0.02670 | 0.00000 | 0.00340 | 0.07880 | 0.01070 | 0.00000 | 0.26230 | 0.00000 | 0.00140 | 0.00000 | 0.98570 | 68.0 | Elapidae | Aird et al. (2017) | Illumina | https://dx.doi.org/10.3390/toxins9060187 |
| Naja_atra | 0.95800 | 0.00000 | 0.00700 | 0.00600 | 0.00100 | 0.00100 | 0.00100 | 0.01200 | 0.00000 | 0.00400 | 0.00000 | 0.99000 | 150.0 | Elapidae | Jiang et al. (2011) | ABI 3100 | https://doi.org/10.1186/1471-2164-12-1 |
| Naja_kaouthia | 0.82000 | 0.00000 | 0.00000 | 0.00500 | 0.00300 | 0.00100 | 0.00200 | 0.13600 | 0.00000 | 0.01100 | 0.00000 | 0.97800 | 150.0 | Elapidae | Xu et al. (2017) | Illumina | https://doi.org/10.1016/j.jprot.2017.02.018 |
| Opheodrys_aestivus | 0.13300 | 0.00000 | 0.00000 | 0.00000 | 0.00000 | 0.00000 | 0.00000 | 0.03600 | 0.00000 | 0.00000 | 0.00000 | 0.16900 | 91.5 | Colubridae | Hargreaves et al. (2014) | Illumina | https://doi.org/10.1016/j.toxicon.2014.10.004 |
| Ophiophagus_hannah | 0.43000 | 0.00000 | 0.08700 | 0.00000 | 0.00800 | 0.01000 | 0.05700 | 0.04000 | 0.00000 | 0.24400 | 0.00700 | 0.88300 | 425.0 | Elapidae | Tan et al. (2015) | Illumina | https://dx.doi.org/10.1186/s12864-015-1828-2 |
| Ovophis_okinavensis | 0.00000 | 0.00000 | 0.00000 | 0.00579 | 0.00008 | 0.00000 | 0.00623 | 0.00000 | 0.00647 | 0.04220 | 0.86176 | 0.92253 | 55.0 | Viperidae | Aird et al. (2013) | Illumina | https://doi.org/10.1186/1471-2164-14-790 |
| Pantherophis_guttatus | 0.01000 | 0.00000 | 0.02200 | 0.00000 | 0.00000 | 0.00000 | 0.00000 | 0.12900 | 0.00000 | 0.00000 | 0.00000 | 0.16100 | 150.0 | Colubridae | Hargreaves et al. (2014) | Illumina | https://doi.org/10.1016/j.toxicon.2014.10.004 |
| Phalotris_mertensi | 0.01800 | 0.00140 | 0.00330 | 0.21600 | 0.00040 | 0.43900 | 0.02300 | 0.00000 | 0.00000 | 0.22040 | 0.00220 | 0.92370 | 100.0 | Colubridae | Campos et al. (2016) | ABI 3100 | https://doi.org/10.1093/gbe/evw149 |
| Philodryas_olfersii | 0.00000 | 0.22400 | 0.10400 | 0.05800 | 0.00000 | 0.00000 | 0.00000 | 0.00000 | 0.00000 | 0.52400 | 0.08900 | 0.99900 | 125.0 | Colubridae | Ching et al. (2006) | ABI 3100 | https://doi.org/10.1016/j.febslet.2006.07.010 |
| Protobothrops_elegans | 0.00000 | 0.01400 | 0.00001 | 0.00200 | 0.00600 | 0.00000 | 0.00500 | 0.00000 | 0.77100 | 0.08100 | 0.10400 | 0.98301 | 120.0 | Viperidae | Aird et al. (2015) | Illumina | https://doi.org/10.1186/s12864-015-1832-6 |
| Protobothrops_flavoviridis | 0.00000 | 0.00000 | 0.03854 | 0.15356 | 0.00960 | 0.00000 | 0.09071 | 0.00000 | 0.32136 | 0.26975 | 0.11054 | 0.99406 | 137.0 | Viperidae | Aird et al. (2013) | Illumina | https://doi.org/10.1186/1471-2164-14-790 |
| Protobothrops_mucrosquamatus | 0.00000 | 0.00000 | 0.01018 | 0.01018 | 0.00647 | 0.00000 | 0.01200 | 0.00000 | 0.25746 | 0.39966 | 0.28076 | 0.97671 | 116.0 | Viperidae | Aird et al. (2017) | Illumina | https://doi.org/10.1093/gbe/evx199 |
| Pseudonaja_textilis | 0.10633 | 0.00000 | 0.03846 | 0.00000 | 0.00452 | 0.01810 | 0.00000 | 0.18778 | 0.00000 | 0.00000 | 0.42534 | 0.78053 | 150.0 | Elapidae | Reeks et al. (2016) | Roche GS FLX | https://doi.org/10.1016/j.jprot.2015.11.019 |
| Sistrurus_catenatus | 0.00830 | 0.00280 | 0.06670 | 0.01390 | 0.06670 | 0.00000 | 0.03610 | 0.00000 | 0.28060 | 0.12220 | 0.37500 | 0.97230 | 73.5 | Viperidae | Pahari et al. (2007) | ABI 3100 | https://doi.org/10.1186/1471-2199-8-115 |
| Thamnodynastes_strigatus | 0.00200 | 0.00000 | 0.01900 | 0.05400 | 0.00000 | 0.00000 | 0.00000 | 0.00000 | 0.00000 | 0.84400 | 0.00700 | 0.92600 | 70.0 | Colubridae | Ching et al. (2011) | ABI 3100 | https://dx.doi.org/10.1021/pr200876c |
Scaled version of this dataset was used in all subsequent analysis
#normalize data
scaled.dat <- dat
scaled.dat[,2:12] <- t(scale(t(scaled.dat[,2:12])))
all_dat<-read.csv("./data/scaleddata/All_25_comps.csv", header = T)
Supplementary Figure 1: Average compositon of each toxin in the venom of 52 species in our studySupplementary Figure 2: Tiles plot showing presence/absensce of each toxin in 52 snake speciesColoured tiles indicate presence of toxin, while white tiles indicate absence. As oberserved from the plot we included components that are found in at least 50% of snakes (Red dashed line). This ensured low retention of structural zeros in our complete dataset.
Higher between clade disparity in phenotypes (disparity between large diversifying lineages) is an indicator of ‘early burst’ evolution (Simpson 1953.; Tran Lucy A. P. 2014). Disparity through time measures instances when disparity was highest within versus among subclades (Harmon et al. 2003; Tran Lucy A. P. 2014). It also provides us an estimate of whether phenotypic diversity occurred early or late in the diversification process. We performed a disparity through time (DTT) analysis to get estimates of when overall disparity in toxin levels arose and the subsequent trends they experienced.
Load data
tree<-read.newick("./Final_tree.tre")
trait<-read.csv("./data/scaleddata/scaled_data_fot_dtt.csv",row.names = 1, header = T)
The following script was repeated for all 11 toxins
trait<-as.matrix(trait)[,'BPP.CNP']
venomdtt <-dtt(tree, trait, index = 'avg.sq', nsim = 5000,
CI = 0.95, plot = F)
Rank envelope function taken from (Murrell 2018)
rank_env_dtt(venomdtt)
## Rank envelope test
## p-value of the test: 0.00379924 (ties method: midrank)
## p-interval : (0.00019996, 0.00739852)
## Rank envelope test
## p-value of the test: 0.00389922 (ties method: midrank)
## p-interval : (0.00019996, 0.00759848)
## Rank envelope test
## p-value of the test: 0.03719256 (ties method: midrank)
## p-interval : (0.03479304, 0.03959208)
## Rank envelope test
## p-value of the test: 0.00379924 (ties method: midrank)
## p-interval : (0.00019996, 0.00739852)
## Rank envelope test
## p-value of the test: 0.00459908 (ties method: midrank)
## p-interval : (0.00019996, 0.0089982)
## Rank envelope test
## p-value of the test: 0.00379924 (ties method: midrank)
## p-interval : (0.00019996, 0.00739852)
## Rank envelope test
## p-value of the test: 0.3285343 (ties method: midrank)
## p-interval : (0.3273345, 0.3297341)
## Rank envelope test
## p-value of the test: 0.00429914 (ties method: midrank)
## p-interval : (0.00019996, 0.00839832)
## Rank envelope test
## p-value of the test: 0.01209758 (ties method: midrank)
## p-interval : (0.00839832, 0.01579684)
## Rank envelope test
## p-value of the test: 0.00429914 (ties method: midrank)
## p-interval : (0.00019996, 0.00839832)
## Rank envelope test
## p-value of the test: 0.2178564 (ties method: midrank)
## p-interval : (0.2159568, 0.219756)
We estimated evolutionary rate dynamics under the Bayesian analysis of macroevolutionary mixtures (BAMM), to observe shifts in rates of gene expression evolution that took place at different points throughout the history of snake venom evolution. Parameters for phenotypic evolution suggested in the online BAMM documentation (http://bamm-project.org/) were used to run the model. The model was run for 108 generations with MCMC write frequency of 104. Priors were obtained using the setBAMMpriors function in BAMMTools (Rabosky et al. 2014).
Supplementary Figure 3: Convergence diagnosis of MCMC chiainsConvergence of MCMC chains were determined by visual inspection, and plotting effective sample size of log-likelihood and number of shifts in each sample, both of which well exceeded the recommended value of 200
mcmcout<- read.csv("./Analysis_scaled/ControlFiles_scaleddata/BPP/mcmc_out.txt", header = T)
plot(mcmcout$logLik ~ mcmcout$generation, type="l")
burnstart <- floor(0.8 * nrow(mcmcout))
postburn <- mcmcout[burnstart:nrow(mcmcout),]
effectiveSize(postburn$N_shifts)
## var1
## 1873.928
effectiveSize(postburn$logLik)
## var1
## 1743.364
plot(postburn$logLik ~ postburn$generation, type="l")
plotPrior(mcmcout, expectedNumberOfShifts = 1)
## var1
## 8001
## var1
## 6696.861
## var1
## 7961.472
## var1
## 9001
## var1
## 9001
## var1
## 8567.747
## var1
## 6775.222
## var1
## 5244.185
## var1
## 3001
## var1
## 3001
## var1
## 2353.79
## var1
## 1715.655
## var1
## 1750.436
## var1
## 1777.745
## var1
## 8014.687
## var1
## 7752.112
## var1
## 8501
## var1
## 7195.953
## var1
## 3196.441
## var1
## 739.902
Bayes factor estimates support the occurrence of at least one rate shift in all toxin families, indicating that toxins families have experienced changes in their evolutionary rates since becoming a part of the venom arsenal. A Bayes factor of 20 and above means that we have enough certainty that the number of rate shifts above the lowest number of shifts in likely.
Supplementary Figure 4: Bayes factor estimates for shift configurationsmcmcout<- read.csv("./Analysis_scaled/ControlFiles_scaleddata/BPP/mcmc_out.txt", header = T)
bfmat<-computeBayesFactors(mcmcout,expectedNumberOfShifts = 1, burnin = 0.8)
# Bayes factor matrix
bfmat
## 3 4 5 6 7 8 9
## 3 1.000000 0.3031136 0.1872172 0.1277006 0.1004248 0.1136676 0.1261433
## 4 3.299094 1.0000000 0.6176471 0.4212963 0.3313107 0.3750000 0.4161585
## 5 5.341390 1.6190476 1.0000000 0.6820988 0.5364078 0.6071429 0.6737805
## 6 7.830816 2.3736264 1.4660633 1.0000000 0.7864078 0.8901099 0.9878049
## 7 9.957704 3.0183150 1.8642534 1.2716049 1.0000000 1.1318681 1.2560976
## 8 8.797583 2.6666667 1.6470588 1.1234568 0.8834951 1.0000000 1.1097561
## 9 7.927492 2.4029304 1.4841629 1.0123457 0.7961165 0.9010989 1.0000000
## 10 4.640483 1.4065934 0.8687783 0.5925926 0.4660194 0.5274725 0.5853659
## 11 3.093656 0.9377289 0.5791855 0.3950617 0.3106796 0.3516484 0.3902439
## 12 3.093656 0.9377289 0.5791855 0.3950617 0.3106796 0.3516484 0.3902439
## 14 6.187311 1.8754579 1.1583710 0.7901235 0.6213592 0.7032967 0.7804878
## 15 12.374622 3.7509158 2.3167421 1.5802469 1.2427184 1.4065934 1.5609756
## 10 11 12 14 15
## 3 0.2154948 0.3232422 0.3232422 0.1616211 0.08081055
## 4 0.7109375 1.0664062 1.0664063 0.5332031 0.26660156
## 5 1.1510417 1.7265625 1.7265625 0.8632813 0.43164063
## 6 1.6875000 2.5312500 2.5312500 1.2656250 0.63281250
## 7 2.1458333 3.2187500 3.2187500 1.6093750 0.80468750
## 8 1.8958333 2.8437500 2.8437500 1.4218750 0.71093750
## 9 1.7083333 2.5625000 2.5625000 1.2812500 0.64062500
## 10 1.0000000 1.5000000 1.5000000 0.7500000 0.37500000
## 11 0.6666667 1.0000000 1.0000000 0.5000000 0.25000000
## 12 0.6666667 1.0000000 1.0000000 0.5000000 0.25000000
## 14 1.3333333 2.0000000 2.0000000 1.0000000 0.50000000
## 15 2.6666667 4.0000000 4.0000000 2.0000000 1.00000000
## 0 1 2 3 4 5
## 0 1.0000 0.002663116 0.001402525 0.0009784736 0.0008116883 0.000697026
## 1 375.5000 1.000000000 0.526647966 0.3674168297 0.3047889610 0.261733271
## 2 713.0000 1.898801598 1.000000000 0.6976516634 0.5787337662 0.496979554
## 3 1022.0000 2.721704394 1.433380084 1.0000000000 0.8295454545 0.712360595
## 4 1232.0000 3.280958722 1.727910238 1.2054794521 1.0000000000 0.858736059
## 5 1434.6667 3.820683533 2.012155213 1.4037834312 1.1645021645 1.000000000
## 6 1562.6667 4.161562361 2.191678354 1.5290280496 1.2683982684 1.089219331
## 7 1664.0000 4.431424767 2.333800842 1.6281800391 1.3506493506 1.159851301
## 8 1664.0000 4.431424767 2.333800842 1.6281800391 1.3506493506 1.159851301
## 9 1877.3333 4.999556147 2.633006078 1.8369210698 1.5238095238 1.308550186
## 10 1450.6667 3.863293387 2.034595605 1.4194390085 1.1774891775 1.011152416
## 11 1536.0000 4.090545939 2.154277700 1.5029354207 1.2467532468 1.070631970
## 12 1024.0000 2.727030626 1.436185133 1.0019569472 0.8311688312 0.713754647
## 13 682.6667 1.818020417 0.957456755 0.6679712981 0.5541125541 0.475836431
## 14 1365.3333 3.636040834 1.914913511 1.3359425962 1.1082251082 0.951672862
## 6 7 8 9 10
## 0 0.0006399317 0.0006009615 0.0006009615 0.0005326705 0.0006893382
## 1 0.2402943686 0.2256610577 0.2256610577 0.2000177557 0.2588465074
## 2 0.4562713311 0.4284855769 0.4284855769 0.3797940341 0.4914981618
## 3 0.6540102389 0.6141826923 0.6141826923 0.5443892045 0.7045036765
## 4 0.7883959044 0.7403846154 0.7403846154 0.6562500000 0.8492647059
## 5 0.9180887372 0.8621794872 0.8621794872 0.7642045455 0.9889705882
## 6 1.0000000000 0.9391025641 0.9391025641 0.8323863636 1.0772058824
## 7 1.0648464164 1.0000000000 1.0000000000 0.8863636364 1.1470588235
## 8 1.0648464164 1.0000000000 1.0000000000 0.8863636364 1.1470588235
## 9 1.2013651877 1.1282051282 1.1282051282 1.0000000000 1.2941176471
## 10 0.9283276451 0.8717948718 0.8717948718 0.7727272727 1.0000000000
## 11 0.9829351536 0.9230769231 0.9230769231 0.8181818182 1.0588235294
## 12 0.6552901024 0.6153846154 0.6153846154 0.5454545455 0.7058823529
## 13 0.4368600683 0.4102564103 0.4102564103 0.3636363636 0.4705882353
## 14 0.8737201365 0.8205128205 0.8205128205 0.7272727273 0.9411764706
## 11 12 13 14
## 0 0.0006510417 0.0009765625 0.001464844 0.0007324219
## 1 0.2444661458 0.3666992188 0.550048828 0.2750244141
## 2 0.4641927083 0.6962890625 1.044433594 0.5222167969
## 3 0.6653645833 0.9980468750 1.497070313 0.7485351563
## 4 0.8020833333 1.2031250000 1.804687500 0.9023437500
## 5 0.9340277778 1.4010416667 2.101562500 1.0507812500
## 6 1.0173611111 1.5260416667 2.289062500 1.1445312500
## 7 1.0833333333 1.6250000000 2.437500000 1.2187500000
## 8 1.0833333333 1.6250000000 2.437500000 1.2187500000
## 9 1.2222222222 1.8333333333 2.750000000 1.3750000000
## 10 0.9444444444 1.4166666667 2.125000000 1.0625000000
## 11 1.0000000000 1.5000000000 2.250000000 1.1250000000
## 12 0.6666666667 1.0000000000 1.500000000 0.7500000000
## 13 0.4444444444 0.6666666667 1.000000000 0.5000000000
## 14 0.8888888889 1.3333333333 2.000000000 1.0000000000
## 1 2 3 4 5 6
## 1 1.00000 0.04133545 0.007011866 0.003128008 0.001852908 0.001314725
## 2 24.19231 1.00000000 0.169633225 0.075673725 0.044826112 0.031806230
## 3 142.61538 5.89507154 1.000000000 0.446102021 0.264253136 0.187500000
## 4 319.69231 13.21462639 2.241639698 1.000000000 0.592360319 0.420307443
## 5 539.69231 22.30842607 3.784250270 1.688161694 1.000000000 0.709546926
## 6 760.61538 31.44038156 5.333333333 2.379210780 1.409350057 1.000000000
## 7 836.92308 34.59459459 5.868392665 2.617901829 1.550741163 1.100323625
## 8 866.46154 35.81558029 6.075512406 2.710298364 1.605473204 1.139158576
## 9 1048.61538 43.34499205 7.352750809 3.280076997 1.942987457 1.378640777
## 10 836.92308 34.59459459 5.868392665 2.617901829 1.550741163 1.100323625
## 11 886.15385 36.62957075 6.213592233 2.771896054 1.641961231 1.165048544
## 12 512.00000 21.16375199 3.590075512 1.601539942 0.948688712 0.673139159
## 13 236.30769 9.76788553 1.656957929 0.739172281 0.437856328 0.310679612
## 14 472.61538 19.53577107 3.313915858 1.478344562 0.875712657 0.621359223
## 15 945.23077 39.07154213 6.627831715 2.956689124 1.751425314 1.242718447
## 16 630.15385 26.04769475 4.418554477 1.971126083 1.167616876 0.828478964
## 7 8 9 10 11
## 1 0.001194853 0.001154119 0.0009536385 0.001194853 0.001128472
## 2 0.028906250 0.027920810 0.0230707160 0.028906250 0.027300347
## 3 0.170404412 0.164595170 0.1360035211 0.170404412 0.160937500
## 4 0.381985294 0.368963068 0.3048708920 0.381985294 0.360763889
## 5 0.644852941 0.622869318 0.5146713615 0.644852941 0.609027778
## 6 0.908823529 0.877840909 0.7253521127 0.908823529 0.858333333
## 7 1.000000000 0.965909091 0.7981220657 1.000000000 0.944444444
## 8 1.035294118 1.000000000 0.8262910798 1.035294118 0.977777778
## 9 1.252941176 1.210227273 1.0000000000 1.252941176 1.183333333
## 10 1.000000000 0.965909091 0.7981220657 1.000000000 0.944444444
## 11 1.058823529 1.022727273 0.8450704225 1.058823529 1.000000000
## 12 0.611764706 0.590909091 0.4882629108 0.611764706 0.577777778
## 13 0.282352941 0.272727273 0.2253521127 0.282352941 0.266666667
## 14 0.564705882 0.545454545 0.4507042254 0.564705882 0.533333333
## 15 1.129411765 1.090909091 0.9014084507 1.129411765 1.066666667
## 16 0.752941176 0.727272727 0.6009389671 0.752941176 0.711111111
## 12 13 14 15 16
## 1 0.001953125 0.004231771 0.002115885 0.001057943 0.001586914
## 2 0.047250601 0.102376302 0.051188151 0.025594076 0.038391113
## 3 0.278545673 0.603515625 0.301757813 0.150878906 0.226318359
## 4 0.624399038 1.352864583 0.676432292 0.338216146 0.507324219
## 5 1.054086538 2.283854167 1.141927083 0.570963542 0.856445313
## 6 1.485576923 3.218750000 1.609375000 0.804687500 1.207031250
## 7 1.634615385 3.541666667 1.770833333 0.885416667 1.328125000
## 8 1.692307692 3.666666667 1.833333333 0.916666667 1.375000000
## 9 2.048076923 4.437500000 2.218750000 1.109375000 1.664062500
## 10 1.634615385 3.541666667 1.770833333 0.885416667 1.328125000
## 11 1.730769231 3.750000000 1.875000000 0.937500000 1.406250000
## 12 1.000000000 2.166666667 1.083333333 0.541666667 0.812500000
## 13 0.461538462 1.000000000 0.500000000 0.250000000 0.375000000
## 14 0.923076923 2.000000000 1.000000000 0.500000000 0.750000000
## 15 1.846153846 4.000000000 2.000000000 1.000000000 1.500000000
## 16 1.230769231 2.666666667 1.333333333 0.666666667 1.000000000
## 1 2 3 4 5
## 1 1.000 0.0006912442 0.0003205128 0.0002042484 0.000161221
## 2 1446.667 1.0000000000 0.4636752137 0.2954793028 0.233233018
## 3 3120.000 2.1566820276 1.0000000000 0.6372549020 0.503009458
## 4 4896.000 3.3843317972 1.5692307692 1.0000000000 0.789337919
## 5 6202.667 4.2875576037 1.9880341880 1.2668845316 1.000000000
## 6 8106.667 5.6036866359 2.5982905983 1.6557734205 1.306964746
## 7 7850.667 5.4267281106 2.5162393162 1.6034858388 1.265692175
## 8 9344.000 6.4589861751 2.9948717949 1.9084967320 1.506448839
## 9 7594.667 5.2497695853 2.4341880342 1.5511982571 1.224419604
## 10 6144.000 4.2470046083 1.9692307692 1.2549019608 0.990541702
## 11 3072.000 2.1235023041 0.9846153846 0.6274509804 0.495270851
## 12 3413.333 2.3594470046 1.0940170940 0.6971677560 0.550300946
## 13 1365.333 0.9437788018 0.4376068376 0.2788671024 0.220120378
## 14 2730.667 1.8875576037 0.8752136752 0.5577342048 0.440240757
## 15 5461.333 3.7751152074 1.7504273504 1.1154684096 0.880481513
## 6 7 8 9 10
## 1 0.0001233553 0.0001273777 0.0001070205 0.0001316713 0.0001627604
## 2 0.1784539474 0.1842730978 0.1548230594 0.1904845506 0.2354600694
## 3 0.3848684211 0.3974184783 0.3339041096 0.4108146067 0.5078125000
## 4 0.6039473684 0.6236413043 0.5239726027 0.6446629213 0.7968750000
## 5 0.7651315789 0.7900815217 0.6638127854 0.8167134831 1.0095486111
## 6 1.0000000000 1.0326086957 0.8675799087 1.0674157303 1.3194444444
## 7 0.9684210526 1.0000000000 0.8401826484 1.0337078652 1.2777777778
## 8 1.1526315789 1.1902173913 1.0000000000 1.2303370787 1.5208333333
## 9 0.9368421053 0.9673913043 0.8127853881 1.0000000000 1.2361111111
## 10 0.7578947368 0.7826086957 0.6575342466 0.8089887640 1.0000000000
## 11 0.3789473684 0.3913043478 0.3287671233 0.4044943820 0.5000000000
## 12 0.4210526316 0.4347826087 0.3652968037 0.4494382022 0.5555555556
## 13 0.1684210526 0.1739130435 0.1461187215 0.1797752809 0.2222222222
## 14 0.3368421053 0.3478260870 0.2922374429 0.3595505618 0.4444444444
## 15 0.6736842105 0.6956521739 0.5844748858 0.7191011236 0.8888888889
## 11 12 13 14 15
## 1 0.0003255208 0.0002929688 0.0007324219 0.0003662109 0.0001831055
## 2 0.4709201389 0.4238281250 1.0595703125 0.5297851563 0.2648925781
## 3 1.0156250000 0.9140625000 2.2851562500 1.1425781250 0.5712890625
## 4 1.5937500000 1.4343750000 3.5859375000 1.7929687500 0.8964843750
## 5 2.0190972222 1.8171875000 4.5429687500 2.2714843750 1.1357421875
## 6 2.6388888889 2.3750000000 5.9375000000 2.9687500000 1.4843750000
## 7 2.5555555556 2.3000000000 5.7500000000 2.8750000000 1.4375000000
## 8 3.0416666667 2.7375000000 6.8437500000 3.4218750000 1.7109375000
## 9 2.4722222222 2.2250000000 5.5625000000 2.7812500000 1.3906250000
## 10 2.0000000000 1.8000000000 4.5000000000 2.2500000000 1.1250000000
## 11 1.0000000000 0.9000000000 2.2500000000 1.1250000000 0.5625000000
## 12 1.1111111111 1.0000000000 2.5000000000 1.2500000000 0.6250000000
## 13 0.4444444444 0.4000000000 1.0000000000 0.5000000000 0.2500000000
## 14 0.8888888889 0.8000000000 2.0000000000 1.0000000000 0.5000000000
## 15 1.7777777778 1.6000000000 4.0000000000 2.0000000000 1.0000000000
## 1 2 3 4 5
## 1 1.000000 0.1021127 0.005484115 0.001942658 0.00108468
## 2 9.793103 1.0000000 0.053706505 0.019024652 0.01062238
## 3 182.344828 18.6197183 1.000000000 0.354233655 0.19778576
## 4 514.758621 52.5633803 2.822995461 1.000000000 0.55834829
## 5 921.931034 94.1408451 5.055975794 1.790996785 1.00000000
## 6 1315.310345 134.3098592 7.213313162 2.555198285 1.42669060
## 7 1600.000000 163.3802817 8.774583964 3.108252947 1.73548773
## 8 2193.655172 224.0000000 12.030257186 4.261521972 2.37941352
## 9 2162.758621 220.8450704 11.860816944 4.201500536 2.34590066
## 10 2560.000000 261.4084507 14.039334342 4.973204716 2.77678037
## 11 2754.206897 281.2394366 15.104387292 5.350482315 2.98743268
## 12 3177.931034 324.5070423 17.428139183 6.173633441 3.44703770
## 13 3248.551724 331.7183099 17.815431165 6.310825295 3.52363854
## 14 3107.310345 317.2957746 17.040847201 6.036441586 3.37043686
## 15 2259.862069 230.7605634 12.393343419 4.390139335 2.45122681
## 16 2259.862069 230.7605634 12.393343419 4.390139335 2.45122681
## 17 6779.586207 692.2816901 37.180030257 13.170418006 7.35368043
## 18 4519.724138 461.5211268 24.786686838 8.780278671 4.90245362
## 6 7 8 9 10
## 1 0.0007602768 0.00062500 0.0004558602 0.0004623724 0.000390625
## 2 0.0074454698 0.00612069 0.0044642857 0.0045280612 0.003825431
## 3 0.1386325503 0.11396552 0.0831237425 0.0843112245 0.071228448
## 4 0.3913590604 0.32172414 0.2346579477 0.2380102041 0.201077586
## 5 0.7009228188 0.57620690 0.4202716298 0.4262755102 0.360129310
## 6 1.0000000000 0.82206897 0.5995975855 0.6081632653 0.513793103
## 7 1.2164429530 1.00000000 0.7293762575 0.7397959184 0.625000000
## 8 1.6677852349 1.37103448 1.0000000000 1.0142857143 0.856896552
## 9 1.6442953020 1.35172414 0.9859154930 1.0000000000 0.844827586
## 10 1.9463087248 1.60000000 1.1670020121 1.1836734694 1.000000000
## 11 2.0939597315 1.72137931 1.2555331992 1.2734693878 1.075862069
## 12 2.4161073826 1.98620690 1.4486921529 1.4693877551 1.241379310
## 13 2.4697986577 2.03034483 1.4808853119 1.5020408163 1.268965517
## 14 2.3624161074 1.94206897 1.4164989940 1.4367346939 1.213793103
## 15 1.7181208054 1.41241379 1.0301810865 1.0448979592 0.882758621
## 16 1.7181208054 1.41241379 1.0301810865 1.0448979592 0.882758621
## 17 5.1543624161 4.23724138 3.0905432596 3.1346938776 2.648275862
## 18 3.4362416107 2.82482759 2.0603621730 2.0897959184 1.765517241
## 11 12 13 14 15
## 1 0.0003630809 0.0003146701 0.0003078295 0.0003218217 0.0004425049
## 2 0.0035556891 0.0030815972 0.0030146060 0.0031516335 0.0043334961
## 3 0.0662059295 0.0573784722 0.0561311141 0.0586825284 0.0806884766
## 4 0.1868990385 0.1619791667 0.1584578804 0.1656605114 0.2277832031
## 5 0.3347355769 0.2901041667 0.2837975543 0.2966974432 0.4079589844
## 6 0.4775641026 0.4138888889 0.4048913043 0.4232954545 0.5820312500
## 7 0.5809294872 0.5034722222 0.4925271739 0.5149147727 0.7080078125
## 8 0.7964743590 0.6902777778 0.6752717391 0.7059659091 0.9707031250
## 9 0.7852564103 0.6805555556 0.6657608696 0.6960227273 0.9570312500
## 10 0.9294871795 0.8055555556 0.7880434783 0.8238636364 1.1328125000
## 11 1.0000000000 0.8666666667 0.8478260870 0.8863636364 1.2187500000
## 12 1.1538461538 1.0000000000 0.9782608696 1.0227272727 1.4062500000
## 13 1.1794871795 1.0222222222 1.0000000000 1.0454545455 1.4375000000
## 14 1.1282051282 0.9777777778 0.9565217391 1.0000000000 1.3750000000
## 15 0.8205128205 0.7111111111 0.6956521739 0.7272727273 1.0000000000
## 16 0.8205128205 0.7111111111 0.6956521739 0.7272727273 1.0000000000
## 17 2.4615384615 2.1333333333 2.0869565217 2.1818181818 3.0000000000
## 18 1.6410256410 1.4222222222 1.3913043478 1.4545454545 2.0000000000
## 16 17 18
## 1 0.0004425049 0.0001475016 0.0002212524
## 2 0.0043334961 0.0014444987 0.0021667480
## 3 0.0806884766 0.0268961589 0.0403442383
## 4 0.2277832031 0.0759277344 0.1138916016
## 5 0.4079589844 0.1359863281 0.2039794922
## 6 0.5820312500 0.1940104167 0.2910156250
## 7 0.7080078125 0.2360026042 0.3540039063
## 8 0.9707031250 0.3235677083 0.4853515625
## 9 0.9570312500 0.3190104167 0.4785156250
## 10 1.1328125000 0.3776041667 0.5664062500
## 11 1.2187500000 0.4062500000 0.6093750000
## 12 1.4062500000 0.4687500000 0.7031250000
## 13 1.4375000000 0.4791666667 0.7187500000
## 14 1.3750000000 0.4583333333 0.6875000000
## 15 1.0000000000 0.3333333333 0.5000000000
## 16 1.0000000000 0.3333333333 0.5000000000
## 17 3.0000000000 1.0000000000 1.5000000000
## 18 2.0000000000 0.6666666667 1.0000000000
## 0 1 2 3 4
## 0 1.000000 0.1065089 0.01294964 0.006276151 0.004136029
## 1 9.388889 1.0000000 0.12158273 0.058926081 0.038832721
## 2 77.222222 8.2248521 1.00000000 0.484658298 0.319393382
## 3 159.333333 16.9704142 2.06330935 1.000000000 0.659007353
## 4 241.777778 25.7514793 3.13093525 1.517433752 1.000000000
## 5 353.777778 37.6804734 4.58129496 2.220362622 1.463235294
## 6 392.888889 41.8461538 5.08776978 2.465829847 1.625000000
## 7 394.666667 42.0355030 5.11079137 2.476987448 1.632352941
## 8 440.888889 46.9585799 5.70935252 2.767085077 1.823529412
## 9 369.777778 39.3846154 4.78848921 2.320781032 1.529411765
## 10 284.444444 30.2958580 3.68345324 1.785216179 1.176470588
## 11 341.333333 36.3550296 4.42014388 2.142259414 1.411764706
## 12 341.333333 36.3550296 4.42014388 2.142259414 1.411764706
## 13 227.555556 24.2366864 2.94676259 1.428172943 0.941176471
## 15 1820.444444 193.8934911 23.57410072 11.425383543 7.529411765
## 5 6 7 8 9 10
## 0 0.002826633 0.002545249 0.002533784 0.002268145 0.002704327 0.003515625
## 1 0.026538945 0.023897059 0.023789414 0.021295363 0.025390625 0.033007812
## 2 0.218278894 0.196549774 0.195664414 0.175151210 0.208834135 0.271484375
## 3 0.450376884 0.405542986 0.403716216 0.361391129 0.430889423 0.560156250
## 4 0.683417085 0.615384615 0.612612613 0.548387097 0.653846154 0.850000000
## 5 1.000000000 0.900452489 0.896396396 0.802419355 0.956730769 1.243750000
## 6 1.110552764 1.000000000 0.995495495 0.891129032 1.062500000 1.381250000
## 7 1.115577889 1.004524887 1.000000000 0.895161290 1.067307692 1.387500000
## 8 1.246231156 1.122171946 1.117117117 1.000000000 1.192307692 1.550000000
## 9 1.045226131 0.941176471 0.936936937 0.838709677 1.000000000 1.300000000
## 10 0.804020101 0.723981900 0.720720721 0.645161290 0.769230769 1.000000000
## 11 0.964824121 0.868778281 0.864864865 0.774193548 0.923076923 1.200000000
## 12 0.964824121 0.868778281 0.864864865 0.774193548 0.923076923 1.200000000
## 13 0.643216080 0.579185520 0.576576577 0.516129032 0.615384615 0.800000000
## 15 5.145728643 4.633484163 4.612612613 4.129032258 4.923076923 6.400000000
## 11 12 13 15
## 0 0.002929687 0.002929688 0.004394531 0.0005493164
## 1 0.027506510 0.027506510 0.041259766 0.0051574707
## 2 0.226236979 0.226236979 0.339355469 0.0424194336
## 3 0.466796875 0.466796875 0.700195313 0.0875244141
## 4 0.708333333 0.708333333 1.062500000 0.1328125000
## 5 1.036458333 1.036458333 1.554687500 0.1943359375
## 6 1.151041667 1.151041667 1.726562500 0.2158203125
## 7 1.156250000 1.156250000 1.734375000 0.2167968750
## 8 1.291666667 1.291666667 1.937500000 0.2421875000
## 9 1.083333333 1.083333333 1.625000000 0.2031250000
## 10 0.833333333 0.833333333 1.250000000 0.1562500000
## 11 1.000000000 1.000000000 1.500000000 0.1875000000
## 12 1.000000000 1.000000000 1.500000000 0.1875000000
## 13 0.666666667 0.666666667 1.000000000 0.1250000000
## 15 5.333333333 5.333333333 8.000000000 1.0000000000
## 1 2 3 4 5 6
## 1 1.000000 0.03659081 0.0196737 0.01790393 0.01856884 0.02628205
## 2 27.329268 1.00000000 0.5376679 0.48930131 0.50747283 0.71826923
## 3 50.829268 1.85988398 1.0000000 0.91004367 0.94384058 1.33589744
## 4 55.853659 2.04373048 1.0988484 1.00000000 1.03713768 1.46794872
## 5 53.853659 1.97054886 1.0595010 0.96419214 1.00000000 1.41538462
## 6 38.048780 1.39223561 0.7485605 0.68122271 0.70652174 1.00000000
## 7 29.268293 1.07095047 0.5758157 0.52401747 0.54347826 0.76923077
## 8 24.195122 0.88531905 0.4760077 0.43318777 0.44927536 0.63589744
## 9 14.048780 0.51405622 0.2763916 0.25152838 0.26086957 0.36923077
## 10 9.365854 0.34270415 0.1842610 0.16768559 0.17391304 0.24615385
## 11 6.243902 0.22846943 0.1228407 0.11179039 0.11594203 0.16410256
## 12 12.487805 0.45693887 0.2456814 0.22358079 0.23188406 0.32820513
## 7 8 9 10 11 12
## 1 0.03416667 0.04133065 0.07118056 0.1067708 0.1601562 0.08007813
## 2 0.93375000 1.12953629 1.94531250 2.9179688 4.3769531 2.18847656
## 3 1.73666667 2.10080645 3.61805556 5.4270833 8.1406250 4.07031250
## 4 1.90833333 2.30846774 3.97569444 5.9635417 8.9453125 4.47265625
## 5 1.84000000 2.22580645 3.83333333 5.7500000 8.6250000 4.31250000
## 6 1.30000000 1.57258065 2.70833333 4.0625000 6.0937500 3.04687500
## 7 1.00000000 1.20967742 2.08333333 3.1250000 4.6875000 2.34375000
## 8 0.82666667 1.00000000 1.72222222 2.5833333 3.8750000 1.93750000
## 9 0.48000000 0.58064516 1.00000000 1.5000000 2.2500000 1.12500000
## 10 0.32000000 0.38709677 0.66666667 1.0000000 1.5000000 0.75000000
## 11 0.21333333 0.25806452 0.44444444 0.6666667 1.0000000 0.50000000
## 12 0.42666667 0.51612903 0.88888889 1.3333333 2.0000000 1.00000000
## 1 2 3 4 5
## 1 1.0000 0.02857143 0.001447876 0.0005215577 0.0002741228
## 2 35.0000 1.00000000 0.050675676 0.0182545202 0.0095942982
## 3 690.6667 19.73333333 1.000000000 0.3602225313 0.1893274854
## 4 1917.3333 54.78095238 2.776061776 1.0000000000 0.5255847953
## 5 3648.0000 104.22857143 5.281853282 1.9026425591 1.0000000000
## 6 5269.3333 150.55238095 7.629343629 2.7482614743 1.4444444444
## 7 7050.6667 201.44761905 10.208494208 3.6773296245 1.9327485380
## 8 8746.6667 249.90476190 12.664092664 4.5618915160 2.3976608187
## 9 10453.3333 298.66666667 15.135135135 5.4520166898 2.8654970760
## 10 10069.3333 287.69523810 14.579150579 5.2517385257 2.7602339181
## 11 10581.3333 302.32380952 15.320463320 5.5187760779 2.9005847953
## 12 10922.6667 312.07619048 15.814671815 5.6968011127 2.9941520468
## 13 13653.3333 390.09523810 19.768339768 7.1210013908 3.7426900585
## 14 9557.3333 273.06666667 13.837837838 4.9847009736 2.6198830409
## 15 8192.0000 234.05714286 11.861003861 4.2726008345 2.2456140351
## 16 5461.3333 156.03809524 7.907335907 2.8484005563 1.4970760234
## 17 10922.6667 312.07619048 15.814671815 5.6968011127 2.9941520468
## 6 7 8 9 10
## 1 0.0001897773 0.0001418306 0.0001143293 9.566327e-05 9.931144e-05
## 2 0.0066422065 0.0049640696 0.0040015244 3.348214e-03 3.475900e-03
## 3 0.1310728745 0.0979576399 0.0789634146 6.607143e-02 6.859110e-02
## 4 0.3638663968 0.2719364599 0.2192073171 1.834184e-01 1.904131e-01
## 5 0.6923076923 0.5173978820 0.4170731707 3.489796e-01 3.622881e-01
## 6 1.0000000000 0.7473524962 0.6024390244 5.040816e-01 5.233051e-01
## 7 1.3380566802 1.0000000000 0.8060975610 6.744898e-01 7.002119e-01
## 8 1.6599190283 1.2405446293 1.0000000000 8.367347e-01 8.686441e-01
## 9 1.9838056680 1.4826021180 1.1951219512 1.000000e+00 1.038136e+00
## 10 1.9109311741 1.4281391831 1.1512195122 9.632653e-01 1.000000e+00
## 11 2.0080971660 1.5007564297 1.2097560976 1.012245e+00 1.050847e+00
## 12 2.0728744939 1.5491679274 1.2487804878 1.044898e+00 1.084746e+00
## 13 2.5910931174 1.9364599092 1.5609756098 1.306122e+00 1.355932e+00
## 14 1.8137651822 1.3555219365 1.0926829268 9.142857e-01 9.491525e-01
## 15 1.5546558704 1.1618759455 0.9365853659 7.836735e-01 8.135593e-01
## 16 1.0364372470 0.7745839637 0.6243902439 5.224490e-01 5.423729e-01
## 17 2.0728744939 1.5491679274 1.2487804878 1.044898e+00 1.084746e+00
## 11 12 13 14 15
## 1 9.450605e-05 9.155273e-05 7.324219e-05 0.0001046317 0.0001220703
## 2 3.307712e-03 3.204346e-03 2.563477e-03 0.0036621094 0.0042724609
## 3 6.527218e-02 6.323242e-02 5.058594e-02 0.0722656250 0.0843098958
## 4 1.811996e-01 1.755371e-01 1.404297e-01 0.2006138393 0.2340494792
## 5 3.447581e-01 3.339844e-01 2.671875e-01 0.3816964286 0.4453125000
## 6 4.979839e-01 4.824219e-01 3.859375e-01 0.5513392857 0.6432291667
## 7 6.663306e-01 6.455078e-01 5.164063e-01 0.7377232143 0.8606770833
## 8 8.266129e-01 8.007813e-01 6.406250e-01 0.9151785714 1.0677083333
## 9 9.879032e-01 9.570313e-01 7.656250e-01 1.0937500000 1.2760416667
## 10 9.516129e-01 9.218750e-01 7.375000e-01 1.0535714286 1.2291666667
## 11 1.000000e+00 9.687500e-01 7.750000e-01 1.1071428571 1.2916666667
## 12 1.032258e+00 1.000000e+00 8.000000e-01 1.1428571429 1.3333333333
## 13 1.290323e+00 1.250000e+00 1.000000e+00 1.4285714286 1.6666666667
## 14 9.032258e-01 8.750000e-01 7.000000e-01 1.0000000000 1.1666666667
## 15 7.741935e-01 7.500000e-01 6.000000e-01 0.8571428571 1.0000000000
## 16 5.161290e-01 5.000000e-01 4.000000e-01 0.5714285714 0.6666666667
## 17 1.032258e+00 1.000000e+00 8.000000e-01 1.1428571429 1.3333333333
## 16 17
## 1 0.0001831055 9.155273e-05
## 2 0.0064086914 3.204346e-03
## 3 0.1264648438 6.323242e-02
## 4 0.3510742188 1.755371e-01
## 5 0.6679687500 3.339844e-01
## 6 0.9648437500 4.824219e-01
## 7 1.2910156250 6.455078e-01
## 8 1.6015625000 8.007812e-01
## 9 1.9140625000 9.570313e-01
## 10 1.8437500000 9.218750e-01
## 11 1.9375000000 9.687500e-01
## 12 2.0000000000 1.000000e+00
## 13 2.5000000000 1.250000e+00
## 14 1.7500000000 8.750000e-01
## 15 1.5000000000 7.500000e-01
## 16 1.0000000000 5.000000e-01
## 17 2.0000000000 1.000000e+00
## 0 1 2 3 4 5
## 0 1.000000 0.4204545 0.004693049 0.002073061 0.001344477 0.001008944
## 1 2.378378 1.0000000 0.011161847 0.004930524 0.003197674 0.002399651
## 2 213.081081 89.5909091 1.000000000 0.441730166 0.286482558 0.214986911
## 3 482.378378 202.8181818 2.263825469 1.000000000 0.648546512 0.486692845
## 4 743.783784 312.7272727 3.490613902 1.541909458 1.000000000 0.750436300
## 5 991.135135 416.7272727 4.651445967 2.054683998 1.332558140 1.000000000
## 6 1101.837838 463.2727273 5.170979198 2.284177499 1.481395349 1.111692845
## 7 1217.729730 512.0000000 5.714865550 2.524428507 1.637209302 1.228621291
## 8 1300.756757 546.9090909 6.104515474 2.696548633 1.748837209 1.312390925
## 9 1383.783784 581.8181818 6.494165398 2.868668758 1.860465116 1.396160558
## 10 1217.729730 512.0000000 5.714865550 2.524428507 1.637209302 1.228621291
## 11 830.270270 349.0909091 3.896499239 1.721201255 1.116279070 0.837696335
## 12 774.918919 325.8181818 3.636732623 1.606454505 1.041860465 0.781849913
## 13 1328.432432 558.5454545 6.234398782 2.753922008 1.786046512 1.340314136
## 14 885.621622 372.3636364 4.156265855 1.835948005 1.190697674 0.893542757
## 15 885.621622 372.3636364 4.156265855 1.835948005 1.190697674 0.893542757
## 6 7 8 9 10
## 0 0.0009075746 0.0008212003 0.0007687832 0.0007226563 0.0008212003
## 1 0.0021585557 0.0019531250 0.0018284574 0.0017187500 0.0019531250
## 2 0.1933869702 0.1749822443 0.1638131649 0.1539843750 0.1749822443
## 3 0.4377943485 0.3961292614 0.3708444149 0.3485937500 0.3961292614
## 4 0.6750392465 0.6107954545 0.5718085106 0.5375000000 0.6107954545
## 5 0.8995290424 0.8139204545 0.7619680851 0.7162500000 0.8139204545
## 6 1.0000000000 0.9048295455 0.8470744681 0.7962500000 0.9048295455
## 7 1.1051805338 1.0000000000 0.9361702128 0.8800000000 1.0000000000
## 8 1.1805337520 1.0681818182 1.0000000000 0.9400000000 1.0681818182
## 9 1.2558869702 1.1363636364 1.0638297872 1.0000000000 1.1363636364
## 10 1.1051805338 1.0000000000 0.9361702128 0.8800000000 1.0000000000
## 11 0.7535321821 0.6818181818 0.6382978723 0.6000000000 0.6818181818
## 12 0.7032967033 0.6363636364 0.5957446809 0.5600000000 0.6363636364
## 13 1.2056514914 1.0909090909 1.0212765957 0.9600000000 1.0909090909
## 14 0.8037676609 0.7272727273 0.6808510638 0.6400000000 0.7272727273
## 15 0.8037676609 0.7272727273 0.6808510638 0.6400000000 0.7272727273
## 11 12 13 14 15
## 0 0.001204427 0.001290458 0.0007527669 0.001129150 0.001129150
## 1 0.002864583 0.003069196 0.0017903646 0.002685547 0.002685547
## 2 0.256640625 0.274972098 0.1604003906 0.240600586 0.240600586
## 3 0.580989583 0.622488839 0.3631184896 0.544677734 0.544677734
## 4 0.895833333 0.959821429 0.5598958333 0.839843750 0.839843750
## 5 1.193750000 1.279017857 0.7460937500 1.119140625 1.119140625
## 6 1.327083333 1.421875000 0.8294270833 1.244140625 1.244140625
## 7 1.466666667 1.571428571 0.9166666667 1.375000000 1.375000000
## 8 1.566666667 1.678571429 0.9791666667 1.468750000 1.468750000
## 9 1.666666667 1.785714286 1.0416666667 1.562500000 1.562500000
## 10 1.466666667 1.571428571 0.9166666667 1.375000000 1.375000000
## 11 1.000000000 1.071428571 0.6250000000 0.937500000 0.937500000
## 12 0.933333333 1.000000000 0.5833333333 0.875000000 0.875000000
## 13 1.600000000 1.714285714 1.0000000000 1.500000000 1.500000000
## 14 1.066666667 1.142857143 0.6666666667 1.000000000 1.000000000
## 15 1.066666667 1.142857143 0.6666666667 1.000000000 1.000000000
## 2 3 4 5 6 7
## 2 1.00000 0.09135802 0.02617925 0.01359628 0.01003254 0.008575402
## 3 10.94595 1.00000000 0.28655660 0.14882411 0.10981562 0.093865884
## 4 38.19820 3.48971193 1.00000000 0.51935326 0.38322487 0.327564895
## 5 73.54955 6.71934156 1.92547170 1.00000000 0.73788865 0.630716934
## 6 99.67568 9.10617284 2.60943396 1.35521803 1.00000000 0.854758962
## 7 116.61261 10.65349794 3.05283019 1.58549731 1.16992046 1.000000000
## 8 113.87387 10.40329218 2.98113208 1.54826066 1.14244396 0.976514215
## 9 107.81982 9.85020576 2.82264151 1.46594806 1.08170644 0.924598269
## 10 85.33333 7.79588477 2.23396226 1.16021558 0.85610991 0.731767614
## 11 85.33333 7.79588477 2.23396226 1.16021558 0.85610991 0.731767614
## 12 36.90090 3.37119342 0.96603774 0.50171485 0.37020969 0.316440049
## 13 64.57658 5.89958848 1.69056604 0.87800098 0.64786696 0.553770087
## 14 18.45045 1.68559671 0.48301887 0.25085742 0.18510484 0.158220025
## 15 73.80180 6.74238683 1.93207547 1.00342969 0.74041938 0.632880099
## 8 9 10 11 12 13
## 2 0.008781646 0.009274733 0.01171875 0.01171875 0.02709961 0.01548549
## 3 0.096123418 0.101520722 0.12827280 0.12827280 0.29663086 0.16950335
## 4 0.335443038 0.354278075 0.44763514 0.44763514 1.03515625 0.59151786
## 5 0.645886076 0.682152406 0.86190878 0.86190878 1.99316406 1.13895089
## 6 0.875316456 0.924465241 1.16807432 1.16807432 2.70117188 1.54352679
## 7 1.024050633 1.081550802 1.36655405 1.36655405 3.16015625 1.80580357
## 8 1.000000000 1.056149733 1.33445946 1.33445946 3.08593750 1.76339286
## 9 0.946835443 1.000000000 1.26351351 1.26351351 2.92187500 1.66964286
## 10 0.749367089 0.791443850 1.00000000 1.00000000 2.31250000 1.32142857
## 11 0.749367089 0.791443850 1.00000000 1.00000000 2.31250000 1.32142857
## 12 0.324050633 0.342245989 0.43243243 0.43243243 1.00000000 0.57142857
## 13 0.567088608 0.598930481 0.75675676 0.75675676 1.75000000 1.00000000
## 14 0.162025316 0.171122995 0.21621622 0.21621622 0.50000000 0.28571429
## 15 0.648101266 0.684491979 0.86486486 0.86486486 2.00000000 1.14285714
## 14 15
## 2 0.05419922 0.0135498
## 3 0.59326172 0.1483154
## 4 2.07031250 0.5175781
## 5 3.98632813 0.9965820
## 6 5.40234375 1.3505859
## 7 6.32031250 1.5800781
## 8 6.17187500 1.5429688
## 9 5.84375000 1.4609375
## 10 4.62500000 1.1562500
## 11 4.62500000 1.1562500
## 12 2.00000000 0.5000000
## 13 3.50000000 0.8750000
## 14 1.00000000 0.2500000
## 15 4.00000000 1.0000000
## 2 3 4 5 6 7
## 2 1.000000 0.2439024 0.1100811 0.06384409 0.04576108 0.03971572
## 3 4.100000 1.0000000 0.4513326 0.26176075 0.18762042 0.16283445
## 4 9.084211 2.2156611 1.0000000 0.57997312 0.41570328 0.36078595
## 5 15.663158 3.8202824 1.7242178 1.00000000 0.71676301 0.62207358
## 6 21.852632 5.3299101 2.4055620 1.39516129 1.00000000 0.86789298
## 7 25.178947 6.1412067 2.7717265 1.60752688 1.15221580 1.00000000
## 8 33.010526 8.0513479 3.6338355 2.10752688 1.51059730 1.31103679
## 9 36.378947 8.8729140 4.0046350 2.32258065 1.66473988 1.44481605
## 10 43.115789 10.5160462 4.7462341 2.75268817 1.97302505 1.71237458
## 11 41.768421 10.1874198 4.5979143 2.66666667 1.91136802 1.65886288
## 12 24.252632 5.9152760 2.6697567 1.54838710 1.10982659 0.96321070
## 13 21.557895 5.2580231 2.3731170 1.37634409 0.98651252 0.85618729
## 14 21.557895 5.2580231 2.3731170 1.37634409 0.98651252 0.85618729
## 15 43.115789 10.5160462 4.7462341 2.75268817 1.97302505 1.71237458
## 16 43.115789 10.5160462 4.7462341 2.75268817 1.97302505 1.71237458
## 8 9 10 11 12 13
## 2 0.03029337 0.02748843 0.02319336 0.02394153 0.04123264 0.04638672
## 3 0.12420281 0.11270255 0.09509277 0.09816028 0.16905382 0.19018555
## 4 0.27519133 0.24971065 0.21069336 0.21748992 0.37456597 0.42138672
## 5 0.47448980 0.43055556 0.36328125 0.37500000 0.64583333 0.72656250
## 6 0.66198980 0.60069444 0.50683594 0.52318548 0.90104167 1.01367188
## 7 0.76275510 0.69212963 0.58398437 0.60282258 1.03819444 1.16796875
## 8 1.00000000 0.90740741 0.76562500 0.79032258 1.36111111 1.53125000
## 9 1.10204082 1.00000000 0.84375000 0.87096774 1.50000000 1.68750000
## 10 1.30612245 1.18518519 1.00000000 1.03225806 1.77777778 2.00000000
## 11 1.26530612 1.14814815 0.96875000 1.00000000 1.72222222 1.93750000
## 12 0.73469388 0.66666667 0.56250000 0.58064516 1.00000000 1.12500000
## 13 0.65306122 0.59259259 0.50000000 0.51612903 0.88888889 1.00000000
## 14 0.65306122 0.59259259 0.50000000 0.51612903 0.88888889 1.00000000
## 15 1.30612245 1.18518519 1.00000000 1.03225806 1.77777778 2.00000000
## 16 1.30612245 1.18518519 1.00000000 1.03225806 1.77777778 2.00000000
## 14 15 16
## 2 0.04638672 0.02319336 0.02319336
## 3 0.19018555 0.09509277 0.09509277
## 4 0.42138672 0.21069336 0.21069336
## 5 0.72656250 0.36328125 0.36328125
## 6 1.01367188 0.50683594 0.50683594
## 7 1.16796875 0.58398438 0.58398438
## 8 1.53125000 0.76562500 0.76562500
## 9 1.68750000 0.84375000 0.84375000
## 10 2.00000000 1.00000000 1.00000000
## 11 1.93750000 0.96875000 0.96875000
## 12 1.12500000 0.56250000 0.56250000
## 13 1.00000000 0.50000000 0.50000000
## 14 1.00000000 0.50000000 0.50000000
## 15 2.00000000 1.00000000 1.00000000
## 16 2.00000000 1.00000000 1.00000000
edata<-getEventData(tree, eventdata="./Analysis_scaled/ControlFiles_scaleddata/BPP/edata_BPP.rds", burnin = 0.1, type= 'diversification')
plot.bammdata(edata, lwd = 1.5, legend = T,labels = T)
distShiftconfigs<-distinctShiftConfigurations(edata, threshold = 0.01, expectedNumberOfShifts = 1)
plot(distShiftconfigs$frequency)
cred_Shift = credibleShiftSet(edata, expectedNumberOfShifts = 1, threshold = 5, set.limit = 0.95)
plot.credibleshiftset(cred_Shift, lwd=1.7, plotmax = 4)
## Omitted 87 plots
cred_Shift$number.distinct
## [1] 91
summary(cred_Shift)
##
## 95 % credible set of rate shift configurations sampled with BAMM
##
## Distinct shift configurations in credible set: 91
##
## Frequency of 9 shift configurations with highest posterior probability:
##
##
## rank probability cumulative Core_shifts
## 1 0.22738631 0.2273863 3
## 2 0.09245377 0.3198401 3
## 3 0.09245377 0.4122939 4
## 4 0.05897051 0.4712644 4
## 5 0.03648176 0.5077461 4
## 6 0.03098451 0.5387306 4
## 7 0.03048476 0.5692154 4
## 8 0.02948526 0.5987006 5
## 9 0.02898551 0.6276862 3
##
## ...omitted 82 additional distinct shift configurations
## from the credible set. You can access the full set from your
## credibleshiftset object
dev.off()
## null device
## 1
best<-getBestShiftConfiguration(edata, expectedNumberOfShifts = 1)
## Processing event data from data.frame
##
## Discarded as burnin: GENERATIONS < 0
## Analyzing 1 samples from posterior
##
## Setting recursive sequence on tree...
##
## Done with recursive sequence
plot.bammdata(best, lwd = 2, legend = T,breaksmethod = "jenks",method = 'polar') + addBAMMshifts(best, cex = 2.5, method = 'polar')
## Error in plot.bammdata(best, lwd = 2, legend = T, breaksmethod = "jenks", : non-numeric argument to binary operator
edata<-getEventData(tree, eventdata="./Analysis_scaled/ControlFiles_scaleddata/CRISP/edata_CRISP.rds", burnin = 0.1, type= 'diversification')
plot.bammdata(edata, lwd = 1.5, legend = T,labels = T)
distShiftconfigs<-distinctShiftConfigurations(edata, threshold = 0.01, expectedNumberOfShifts = 1)
plot(distShiftconfigs$frequency)
cred_Shift = credibleShiftSet(edata, expectedNumberOfShifts = 1, threshold = 5, set.limit = 0.95)
plot.credibleshiftset(cred_Shift, lwd=1.7, plotmax = 4)
## Omitted 8 plots
cred_Shift$number.distinct
## [1] 12
summary(cred_Shift)
##
## 95 % credible set of rate shift configurations sampled with BAMM
##
## Distinct shift configurations in credible set: 12
##
## Frequency of 9 shift configurations with highest posterior probability:
##
##
## rank probability cumulative Core_shifts
## 1 0.37607799 0.3760780 1
## 2 0.16535433 0.5414323 1
## 3 0.12773403 0.6691664 1
## 4 0.09423822 0.7634046 2
## 5 0.06411699 0.8275216 1
## 6 0.03212098 0.8596425 2
## 7 0.02887139 0.8885139 2
## 8 0.02737158 0.9158855 2
## 9 0.01449819 0.9303837 2
##
## ...omitted 3 additional distinct shift configurations
## from the credible set. You can access the full set from your
## credibleshiftset object
dev.off()
## null device
## 1
best<-getBestShiftConfiguration(edata, expectedNumberOfShifts = 1)
## Processing event data from data.frame
##
## Discarded as burnin: GENERATIONS < 0
## Analyzing 1 samples from posterior
##
## Setting recursive sequence on tree...
##
## Done with recursive sequence
plot.bammdata(best, lwd = 2, legend = T,breaksmethod = "jenks", method = 'polar') + addBAMMshifts(best, cex = 2.5, method = 'polar')
## Error in plot.bammdata(best, lwd = 2, legend = T, breaksmethod = "jenks", : non-numeric argument to binary operator
edata<-getEventData(tree, eventdata="./Analysis_scaled/ControlFiles_scaleddata/CTL/event_dataCTL.txt", burnin = 0.1, type= 'diversification')
plot.bammdata(edata, lwd = 1.5, legend = T,labels = T)
distShiftconfigs<-distinctShiftConfigurations(edata, threshold = 0.01, expectedNumberOfShifts = 1)
plot(distShiftconfigs$frequency)
cred_Shift = credibleShiftSet(edata, expectedNumberOfShifts = 1, threshold = 5, set.limit = 0.95)
plot.credibleshiftset(cred_Shift, lwd=1.7, plotmax = 4)
## Omitted 139 plots
cred_Shift$number.distinct
## [1] 143
summary(cred_Shift)
##
## 95 % credible set of rate shift configurations sampled with BAMM
##
## Distinct shift configurations in credible set: 143
##
## Frequency of 9 shift configurations with highest posterior probability:
##
##
## rank probability cumulative Core_shifts
## 1 0.18986779 0.1898678 3
## 2 0.12143095 0.3112987 2
## 3 0.07076991 0.3820687 3
## 4 0.06354849 0.4456172 3
## 5 0.04655038 0.4921675 3
## 6 0.04243973 0.5346073 2
## 7 0.03188535 0.5664926 4
## 8 0.02210865 0.5886013 3
## 9 0.01733141 0.6059327 4
##
## ...omitted 134 additional distinct shift configurations
## from the credible set. You can access the full set from your
## credibleshiftset object
dev.off()
## null device
## 1
best<-getBestShiftConfiguration(edata, expectedNumberOfShifts = 1)
## Processing event data from data.frame
##
## Discarded as burnin: GENERATIONS < 0
## Analyzing 1 samples from posterior
##
## Setting recursive sequence on tree...
##
## Done with recursive sequence
plot.bammdata(best, lwd = 2, legend = T,breaksmethod = "jenks",method = 'polar') + addBAMMshifts(best, cex = 2.5,method = 'polar')
## Error in plot.bammdata(best, lwd = 2, legend = T, breaksmethod = "jenks", : non-numeric argument to binary operator
edata<-getEventData(tree, eventdata="./Analysis_scaled/ControlFiles_scaleddata/GF/event_dataGF.txt", burnin = 0.1, type= 'diversification')
plot.bammdata(edata, lwd = 1.5, legend = T,labels = T)
distShiftconfigs<-distinctShiftConfigurations(edata, threshold = 0.01, expectedNumberOfShifts = 1)
plot(distShiftconfigs$frequency)
cred_Shift = credibleShiftSet(edata, expectedNumberOfShifts = 1, threshold = 5, set.limit = 0.95)
plot.credibleshiftset(cred_Shift, lwd=1.7, plotmax = 4)
## Omitted 110 plots
cred_Shift$number.distinct
## [1] 114
summary(cred_Shift)
##
## 95 % credible set of rate shift configurations sampled with BAMM
##
## Distinct shift configurations in credible set: 114
##
## Frequency of 9 shift configurations with highest posterior probability:
##
##
## rank probability cumulative Core_shifts
## 1 0.25452727 0.2545273 2
## 2 0.17298078 0.4275081 2
## 3 0.05799356 0.4855016 2
## 4 0.05754916 0.5430508 2
## 5 0.04221753 0.5852683 2
## 6 0.03910677 0.6243751 4
## 7 0.02377514 0.6481502 3
## 8 0.02377514 0.6719253 3
## 9 0.02321964 0.6951450 3
##
## ...omitted 105 additional distinct shift configurations
## from the credible set. You can access the full set from your
## credibleshiftset object
dev.off()
## null device
## 1
best<-getBestShiftConfiguration(edata, expectedNumberOfShifts = 1)
## Processing event data from data.frame
##
## Discarded as burnin: GENERATIONS < 0
## Analyzing 1 samples from posterior
##
## Setting recursive sequence on tree...
##
## Done with recursive sequence
plot.bammdata(best, lwd = 2, legend = T,breaksmethod = "jenks",method = 'polar') + addBAMMshifts(best, cex = 2.5,method = 'polar')
## Error in plot.bammdata(best, lwd = 2, legend = T, breaksmethod = "jenks", : non-numeric argument to binary operator
edata<-getEventData(tree, eventdata="./Analysis_scaled/ControlFiles_scaleddata/KUN/event_dataKUN.txt", burnin = 0.1, type= 'diversification')
plot.bammdata(edata, lwd = 1.5, legend = T,labels = T)
distShiftconfigs<-distinctShiftConfigurations(edata, threshold = 0.01, expectedNumberOfShifts = 1)
plot(distShiftconfigs$frequency)
cred_Shift = credibleShiftSet(edata, expectedNumberOfShifts = 1, threshold = 5, set.limit = 0.95)
plot.credibleshiftset(cred_Shift, lwd=1.7, plotmax = 4)
## Omitted 317 plots
cred_Shift$number.distinct
## [1] 321
summary(cred_Shift)
##
## 95 % credible set of rate shift configurations sampled with BAMM
##
## Distinct shift configurations in credible set: 321
##
## Frequency of 9 shift configurations with highest posterior probability:
##
##
## rank probability cumulative Core_shifts
## 1 0.23447069 0.2344707 3
## 2 0.09123860 0.3257093 3
## 3 0.05436820 0.3800775 4
## 4 0.03237095 0.4124484 3
## 5 0.03187102 0.4443195 4
## 6 0.02824647 0.4725659 4
## 7 0.02287214 0.4954381 3
## 8 0.01987252 0.5153106 3
## 9 0.01424822 0.5295588 3
##
## ...omitted 312 additional distinct shift configurations
## from the credible set. You can access the full set from your
## credibleshiftset object
dev.off()
## null device
## 1
best<-getBestShiftConfiguration(edata, expectedNumberOfShifts = 1)
## Processing event data from data.frame
##
## Discarded as burnin: GENERATIONS < 0
## Analyzing 1 samples from posterior
##
## Setting recursive sequence on tree...
##
## Done with recursive sequence
plot.bammdata(best, lwd = 2, legend = T,breaksmethod = "jenks",method = 'polar') + addBAMMshifts(best, cex = 2.5,method = 'polar')
## Error in plot.bammdata(best, lwd = 2, legend = T, breaksmethod = "jenks", : non-numeric argument to binary operator
edata<-getEventData(tree, eventdata="./Analysis_scaled/ControlFiles_scaleddata/LAAO/event_dataLAAO.txt", burnin = 0.1, type= 'diversification')
plot.bammdata(edata, lwd = 1.5, legend = T,labels = T)
distShiftconfigs<-distinctShiftConfigurations(edata, threshold = 0.01, expectedNumberOfShifts = 1)
plot(distShiftconfigs$frequency)
cred_Shift = credibleShiftSet(edata, expectedNumberOfShifts = 1, threshold = 5, set.limit = 0.95)
plot.credibleshiftset(cred_Shift, lwd=1.7, plotmax = 4)
## Omitted 42 plots
cred_Shift$number.distinct
## [1] 46
summary(cred_Shift)
##
## 95 % credible set of rate shift configurations sampled with BAMM
##
## Distinct shift configurations in credible set: 46
##
## Frequency of 9 shift configurations with highest posterior probability:
##
##
## rank probability cumulative Core_shifts
## 1 0.23058980 0.2305898 2
## 2 0.11262912 0.3432189 2
## 3 0.11262912 0.4558481 2
## 4 0.06864379 0.5244918 0
## 5 0.05598134 0.5804732 3
## 6 0.04798401 0.6284572 2
## 7 0.04265245 0.6711096 1
## 8 0.02765745 0.6987671 2
## 9 0.02465845 0.7234255 3
##
## ...omitted 37 additional distinct shift configurations
## from the credible set. You can access the full set from your
## credibleshiftset object
dev.off()
## null device
## 1
best<-getBestShiftConfiguration(edata, expectedNumberOfShifts = 1)
## Processing event data from data.frame
##
## Discarded as burnin: GENERATIONS < 0
## Analyzing 1 samples from posterior
##
## Setting recursive sequence on tree...
##
## Done with recursive sequence
plot.bammdata(best, lwd = 2, legend = T,breaksmethod = "jenks",method = 'polar') + addBAMMshifts(best, cex = 2.5,method = 'polar')
## Error in plot.bammdata(best, lwd = 2, legend = T, breaksmethod = "jenks", : non-numeric argument to binary operator
edata<-getEventData(tree, eventdata="./Analysis_scaled/ControlFiles_scaleddata/vPLA2ePLA2/event_data_vPLA2.txt", burnin = 0.1, type= 'diversification')
distShiftconfigs<-distinctShiftConfigurations(edata, threshold = 0.01, expectedNumberOfShifts = 1)
plot(distShiftconfigs$frequency)
cred_Shift = credibleShiftSet(edata, expectedNumberOfShifts = 1, threshold = 5, set.limit = 0.95)
plot.credibleshiftset(cred_Shift, lwd=1.7, plotmax = 4)
## Omitted 9 plots
cred_Shift$number.distinct
## [1] 13
summary(cred_Shift)
##
## 95 % credible set of rate shift configurations sampled with BAMM
##
## Distinct shift configurations in credible set: 13
##
## Frequency of 9 shift configurations with highest posterior probability:
##
##
## rank probability cumulative Core_shifts
## 1 0.56805399 0.5680540 2
## 2 0.16222972 0.7302837 3
## 3 0.04911886 0.7794026 3
## 4 0.04424447 0.8236470 1
## 5 0.02612173 0.8497688 2
## 6 0.02124734 0.8710161 4
## 7 0.02037245 0.8913886 1
## 8 0.01687289 0.9082615 2
## 9 0.01399825 0.9222597 3
##
## ...omitted 4 additional distinct shift configurations
## from the credible set. You can access the full set from your
## credibleshiftset object
dev.off()
## null device
## 1
best<-getBestShiftConfiguration(edata, expectedNumberOfShifts = 1)
## Processing event data from data.frame
##
## Discarded as burnin: GENERATIONS < 0
## Analyzing 1 samples from posterior
##
## Setting recursive sequence on tree...
##
## Done with recursive sequence
plot.bammdata(best, lwd = 2, legend = T,breaksmethod = "jenks",method = 'polar') + addBAMMshifts(best, cex = 2.5,method = 'polar')
## Error in plot.bammdata(best, lwd = 2, legend = T, breaksmethod = "jenks", : non-numeric argument to binary operator
edata<-getEventData(tree, eventdata="./Analysis_scaled/ControlFiles_scaleddata/vPLA2ePLA2/event_data_ePLA2.txt", burnin = 0.1, type= 'diversification')
distShiftconfigs<-distinctShiftConfigurations(edata, threshold = 0.01, expectedNumberOfShifts = 1)
plot(distShiftconfigs$frequency)
cred_Shift = credibleShiftSet(edata, expectedNumberOfShifts = 1, threshold = 5, set.limit = 0.95)
plot.credibleshiftset(cred_Shift, lwd=1.7, plotmax = 4)
## Omitted 352 plots
cred_Shift$number.distinct
## [1] 356
summary(cred_Shift)
##
## 95 % credible set of rate shift configurations sampled with BAMM
##
## Distinct shift configurations in credible set: 356
##
## Frequency of 9 shift configurations with highest posterior probability:
##
##
## rank probability cumulative Core_shifts
## 1 0.14885639 0.1488564 3
## 2 0.10323710 0.2520935 3
## 3 0.06249219 0.3145857 4
## 4 0.05311836 0.3677040 3
## 5 0.02987127 0.3975753 3
## 6 0.02849644 0.4260717 3
## 7 0.02412198 0.4501937 4
## 8 0.02374703 0.4739408 4
## 9 0.01887264 0.4928134 3
##
## ...omitted 347 additional distinct shift configurations
## from the credible set. You can access the full set from your
## credibleshiftset object
dev.off()
## null device
## 1
best<-getBestShiftConfiguration(edata, expectedNumberOfShifts = 1)
## Processing event data from data.frame
##
## Discarded as burnin: GENERATIONS < 0
## Analyzing 1 samples from posterior
##
## Setting recursive sequence on tree...
##
## Done with recursive sequence
plot.bammdata(best, lwd = 2, legend = T,breaksmethod = "jenks",method = 'polar') + addBAMMshifts(best, cex = 2.5,method = 'polar')
## Error in plot.bammdata(best, lwd = 2, legend = T, breaksmethod = "jenks", : non-numeric argument to binary operator
edata<-getEventData(tree, eventdata="./Analysis_scaled/ControlFiles_scaleddata/SVMP/event_dataSVMP.txt", burnin = 0.1, type= 'diversification')
distShiftconfigs<-distinctShiftConfigurations(edata, threshold = 0.01, expectedNumberOfShifts = 1)
plot(distShiftconfigs$frequency)
cred_Shift = credibleShiftSet(edata, expectedNumberOfShifts = 1, threshold = 5, set.limit = 0.95)
plot.credibleshiftset(cred_Shift, lwd=1.7, plotmax = 4)
## Omitted 0 plots
cred_Shift$number.distinct
## [1] 4
summary(cred_Shift)
##
## 95 % credible set of rate shift configurations sampled with BAMM
##
## Distinct shift configurations in credible set: 4
##
## Frequency of 4 shift configurations with highest posterior probability:
##
##
## rank probability cumulative Core_shifts
## 1 0.84672391 0.8467239 2
## 2 0.05599341 0.9027173 3
## 3 0.03623103 0.9389484 3
## 4 0.02929067 0.9682390 3
dev.off()
## null device
## 1
best<-getBestShiftConfiguration(edata, expectedNumberOfShifts = 1)
## Processing event data from data.frame
##
## Discarded as burnin: GENERATIONS < 0
## Analyzing 1 samples from posterior
##
## Setting recursive sequence on tree...
##
## Done with recursive sequence
plot.bammdata(best, lwd = 2, legend = T,breaksmethod = "jenks",method = 'polar') + addBAMMshifts(best, cex = 2.5,method = 'polar')
## Error in plot.bammdata(best, lwd = 2, legend = T, breaksmethod = "jenks", : non-numeric argument to binary operator
edata<-getEventData(tree, eventdata="./Analysis_scaled/ControlFiles_scaleddata/SVSP/event_dataLAAO.txt", burnin = 0.1, type= 'diversification')
distShiftconfigs<-distinctShiftConfigurations(edata, threshold = 0.01, expectedNumberOfShifts = 1)
plot(distShiftconfigs$frequency)
cred_Shift = credibleShiftSet(edata, expectedNumberOfShifts = 1, threshold = 5, set.limit = 0.95)
plot.credibleshiftset(cred_Shift, lwd=1.7, plotmax = 4)
## Omitted 36 plots
cred_Shift$number.distinct
## [1] 40
summary(cred_Shift)
##
## 95 % credible set of rate shift configurations sampled with BAMM
##
## Distinct shift configurations in credible set: 40
##
## Frequency of 9 shift configurations with highest posterior probability:
##
##
## rank probability cumulative Core_shifts
## 1 0.18821315 0.1882132 4
## 2 0.16303964 0.3512528 3
## 3 0.10692860 0.4581814 4
## 4 0.09398894 0.5521703 3
## 5 0.04246559 0.5946359 2
## 6 0.04070109 0.6353370 3
## 7 0.03093754 0.6662746 5
## 8 0.03034937 0.6966239 5
## 9 0.02623221 0.7228561 4
##
## ...omitted 31 additional distinct shift configurations
## from the credible set. You can access the full set from your
## credibleshiftset object
dev.off()
## null device
## 1
best<-getBestShiftConfiguration(edata, expectedNumberOfShifts = 1)
## Processing event data from data.frame
##
## Discarded as burnin: GENERATIONS < 0
## Analyzing 1 samples from posterior
##
## Setting recursive sequence on tree...
##
## Done with recursive sequence
plot.bammdata(best, lwd = 2, legend = T,breaksmethod = "jenks",method = 'polar') + addBAMMshifts(best, cex = 2.5,method = 'polar')
## Error in plot.bammdata(best, lwd = 2, legend = T, breaksmethod = "jenks", : non-numeric argument to binary operator
edata<-getEventData(tree, eventdata="./Analysis_scaled/ControlFiles_scaleddata/TFTx/event_dataTFTx.txt", burnin = 0.1, type= 'diversification')
distShiftconfigs<-distinctShiftConfigurations(edata, threshold = 0.01, expectedNumberOfShifts = 1)
plot(distShiftconfigs$frequency)
cred_Shift = credibleShiftSet(edata, expectedNumberOfShifts = 1, threshold = 5, set.limit = 0.95)
plot.credibleshiftset(cred_Shift, lwd=1.7, plotmax = 4)
## Omitted 139 plots
cred_Shift$number.distinct
## [1] 143
summary(cred_Shift)
##
## 95 % credible set of rate shift configurations sampled with BAMM
##
## Distinct shift configurations in credible set: 143
##
## Frequency of 9 shift configurations with highest posterior probability:
##
##
## rank probability cumulative Core_shifts
## 1 0.17520620 0.1752062 2
## 2 0.17270682 0.3479130 3
## 3 0.07273182 0.4206448 2
## 4 0.05723569 0.4778805 4
## 5 0.04098975 0.5188703 4
## 6 0.03924019 0.5581105 3
## 7 0.02624344 0.5843539 3
## 8 0.02549363 0.6098475 3
## 9 0.01599600 0.6258435 4
##
## ...omitted 134 additional distinct shift configurations
## from the credible set. You can access the full set from your
## credibleshiftset object
dev.off()
## null device
## 1
best<-getBestShiftConfiguration(edata, expectedNumberOfShifts = 1)
## Processing event data from data.frame
##
## Discarded as burnin: GENERATIONS < 0
## Analyzing 1 samples from posterior
##
## Setting recursive sequence on tree...
##
## Done with recursive sequence
plot.bammdata(best, lwd = 2, legend = T, breaksmethod = "jenks",method = 'polar') + addBAMMshifts(best, cex = 2.5,method = 'polar')
## Error in plot.bammdata(best, lwd = 2, legend = T, breaksmethod = "jenks", : non-numeric argument to binary operator
Since the early burst model states that branching events account for most of the phenotypic diversity amongst species (Simpson 1953.; Ingram et al. 2012), we expect the rate of trait evolution to be high immediately after major lineages diverge. To identify these increases we estimated the evolutionary rate of each toxin family after the split of the three venomous families. Our estimates of ‘rate through time’ revealed that toxin families show unique evolutionary rates and rate dynamics in each venomous snake family (Fig. 4)
st <- max(branching.times(tree))
plotRateThroughTime(edataBPP, intervalCol="blue", avgCol="blue", start.time=st, node=97, ylim=c(0,.08),cex.axis=1)+
text(x=30, y= 0.008, label="Colubrids only", font=4, cex=2.0, pos=4)
plotRateThroughTime(edataBPP, intervalCol="red", avgCol="red", start.time=st, node=54, ylim=c(0,.08),cex.axis=1)+
text(x=30, y= 0.008, label="Vipers only", font=4, cex=2.0, pos=4)
plotRateThroughTime(edataBPP, intervalCol="green", avgCol="green", start.time=st, node=85, ylim=c(0,.08),cex.axis=1)+
text(x=30, y= 0.008, label="Elapids only", font=4, cex=2.0, pos=4)
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We fit a number of trait evolution models to our data to understand which evolutionary process best describes snake venom evolution. Along with conventional models, like Brownian motion (BM), Ornstein-Uhlenbeck (OU), we tested a specific Early burst (EB) model implemented in geiger (Pennell et al. 2014).
Load libraries
library(geiger)
library(phytools)
fitContinuous from geigerLoad data
tree<-read.newick("./Final_tree.tre")
trait<-read.csv("./data/scaleddata/scaled_data_fot_dtt.csv", row.names = 1, header = T)
dat<-setNames(trait$BPP.CNP,rownames(trait))
fitBM<-fitContinuous(tree,dat)
fitOU<-fitContinuous(tree,dat,model="OU")
fitEB<-fitContinuous(tree,dat,model="EB")
fitBM$opt
## $sigsq
## [1] 0.03763935
##
## $z0
## [1] -0.235386
##
## $lnL
## [1] -70.77994
##
## $method
## [1] "Brent"
##
## $k
## [1] 2
##
## $aic
## [1] 145.5599
##
## $aicc
## [1] 145.8048
fitOU$opt
## $alpha
## [1] 2.718282
##
## $sigsq
## [1] 2.805926
##
## $z0
## [1] -0.05130243
##
## $lnL
## [1] -56.58804
##
## $method
## [1] "L-BFGS-B"
##
## $k
## [1] 3
##
## $aic
## [1] 119.1761
##
## $aicc
## [1] 119.6761
fitEB$opt
## $a
## [1] -1e-06
##
## $sigsq
## [1] 0.03764146
##
## $z0
## [1] -0.2353863
##
## $lnL
## [1] -70.78014
##
## $method
## [1] "L-BFGS-B"
##
## $k
## [1] 3
##
## $aic
## [1] 147.5603
##
## $aicc
## [1] 148.0603
aic.vals<-setNames(c(fitBM$opt$aicc,fitOU$opt$aicc,fitEB$opt$aicc),c("BM","OU","EB"))
aic.vals
## BM OU EB
## 145.8048 119.6761 148.0603
aic.w(aic.vals)
## BM OU EB
## 0.00000212 0.99999719 0.00000069
fitBM$opt
## $sigsq
## [1] 0.00281511
##
## $z0
## [1] -0.2990053
##
## $lnL
## [1] -3.36067
##
## $method
## [1] "Brent"
##
## $k
## [1] 2
##
## $aic
## [1] 10.72134
##
## $aicc
## [1] 10.96624
fitOU$opt
## $alpha
## [1] 0.09424551
##
## $sigsq
## [1] 0.010191
##
## $z0
## [1] -0.3486082
##
## $lnL
## [1] 3.560175
##
## $method
## [1] "L-BFGS-B"
##
## $k
## [1] 3
##
## $aic
## [1] -1.12035
##
## $aicc
## [1] -0.6203504
fitEB$opt
## $a
## [1] -1e-06
##
## $sigsq
## [1] 0.002815263
##
## $z0
## [1] -0.2990054
##
## $lnL
## [1] -3.360821
##
## $method
## [1] "L-BFGS-B"
##
## $k
## [1] 3
##
## $aic
## [1] 12.72164
##
## $aicc
## [1] 13.22164
aic.vals<-setNames(c(fitBM$opt$aicc,fitOU$opt$aicc,fitEB$opt$aicc),c("BM","OU","EB"))
aic.vals
## BM OU EB
## 10.9662381 -0.6203504 13.2216415
aic.w(aic.vals)
## BM OU EB
## 0.00303568 0.99598144 0.00098288
fitBM$opt
## $sigsq
## [1] 0.00965261
##
## $z0
## [1] -0.1509853
##
## $lnL
## [1] -35.39857
##
## $method
## [1] "Brent"
##
## $k
## [1] 2
##
## $aic
## [1] 74.79714
##
## $aicc
## [1] 75.04204
fitOU$opt
## $alpha
## [1] 0.04778383
##
## $sigsq
## [1] 0.02154569
##
## $z0
## [1] -0.172549
##
## $lnL
## [1] -30.58365
##
## $method
## [1] "L-BFGS-B"
##
## $k
## [1] 3
##
## $aic
## [1] 67.16731
##
## $aicc
## [1] 67.66731
fitEB$opt
## $a
## [1] -1e-06
##
## $sigsq
## [1] 0.009653122
##
## $z0
## [1] -0.150985
##
## $lnL
## [1] -35.39869
##
## $method
## [1] "L-BFGS-B"
##
## $k
## [1] 3
##
## $aic
## [1] 76.79738
##
## $aicc
## [1] 77.29738
aic.vals<-setNames(c(fitBM$opt$aicc,fitOU$opt$aicc,fitEB$opt$aicc),c("BM","OU","EB"))
aic.vals
## BM OU EB
## 75.04204 67.66731 77.29738
aic.w(aic.vals)
## BM OU EB
## 0.02423460 0.96791855 0.00784685
fitBM$opt
## $sigsq
## [1] 0.00559709
##
## $z0
## [1] -0.3978027
##
## $lnL
## [1] -21.22905
##
## $method
## [1] "Brent"
##
## $k
## [1] 2
##
## $aic
## [1] 46.45811
##
## $aicc
## [1] 46.70301
fitOU$opt
## $alpha
## [1] 2.718282
##
## $sigsq
## [1] 0.4569515
##
## $z0
## [1] -0.3991772
##
## $lnL
## [1] -9.400349
##
## $method
## [1] "L-BFGS-B"
##
## $k
## [1] 3
##
## $aic
## [1] 24.8007
##
## $aicc
## [1] 25.3007
fitEB$opt
## $a
## [1] -1e-06
##
## $sigsq
## [1] 0.005597395
##
## $z0
## [1] -0.3978025
##
## $lnL
## [1] -21.22921
##
## $method
## [1] "L-BFGS-B"
##
## $k
## [1] 3
##
## $aic
## [1] 48.45842
##
## $aicc
## [1] 48.95842
aic.vals<-setNames(c(fitBM$opt$aicc,fitOU$opt$aicc,fitEB$opt$aicc),
c("BM","OU","EB"))
aic.vals
## BM OU EB
## 46.70301 25.30070 48.95842
aic.w(aic.vals)
## BM OU EB
## 0.00002252 0.99997019 0.00000729
fitBM$opt
## $sigsq
## [1] 0.0066864
##
## $z0
## [1] -0.2439804
##
## $lnL
## [1] -25.8526
##
## $method
## [1] "Brent"
##
## $k
## [1] 2
##
## $aic
## [1] 55.70521
##
## $aicc
## [1] 55.95011
fitOU$opt
## $alpha
## [1] 3.115799e-17
##
## $sigsq
## [1] 0.006686401
##
## $z0
## [1] -0.2439804
##
## $lnL
## [1] -25.8526
##
## $method
## [1] "subplex"
##
## $k
## [1] 3
##
## $aic
## [1] 57.70521
##
## $aicc
## [1] 58.20521
fitEB$opt
## $a
## [1] -0.0007395406
##
## $sigsq
## [1] 0.006929684
##
## $z0
## [1] -0.2440186
##
## $lnL
## [1] -25.85224
##
## $method
## [1] "subplex"
##
## $k
## [1] 3
##
## $aic
## [1] 57.70449
##
## $aicc
## [1] 58.20449
aic.vals<-setNames(c(fitBM$opt$aicc,fitOU$opt$aicc,fitEB$opt$aicc),
c("BM","OU","EB"))
aic.vals
## BM OU EB
## 55.95011 58.20521 58.20449
aic.w(aic.vals)
## BM OU EB
## 0.6068818 0.1965237 0.1965946
fitBM$opt
## $sigsq
## [1] 0.001368342
##
## $z0
## [1] -0.3831869
##
## $lnL
## [1] 15.39577
##
## $method
## [1] "Brent"
##
## $k
## [1] 2
##
## $aic
## [1] -26.79153
##
## $aicc
## [1] -26.54663
fitOU$opt
## $alpha
## [1] 0.2403901
##
## $sigsq
## [1] 0.0104923
##
## $z0
## [1] -0.3780048
##
## $lnL
## [1] 25.8697
##
## $method
## [1] "L-BFGS-B"
##
## $k
## [1] 3
##
## $aic
## [1] -45.7394
##
## $aicc
## [1] -45.2394
fitEB$opt
## $a
## [1] -1e-06
##
## $sigsq
## [1] 0.001368417
##
## $z0
## [1] -0.3831867
##
## $lnL
## [1] 15.39561
##
## $method
## [1] "L-BFGS-B"
##
## $k
## [1] 3
##
## $aic
## [1] -24.79121
##
## $aicc
## [1] -24.29121
aic.vals<-setNames(c(fitBM$opt$aicc,fitOU$opt$aicc,fitEB$opt$aicc),
c("BM","OU","EB"))
aic.vals
## BM OU EB
## -26.54663 -45.23940 -24.29121
aic.w(aic.vals)
## BM OU EB
## 0.00008727 0.99988447 0.00002826
fitBM$opt
## $sigsq
## [1] 0.04095841
##
## $z0
## [1] 1.335358
##
## $lnL
## [1] -72.97712
##
## $method
## [1] "Brent"
##
## $k
## [1] 2
##
## $aic
## [1] 149.9542
##
## $aicc
## [1] 150.1991
fitOU$opt
## $alpha
## [1] 0.007577426
##
## $sigsq
## [1] 0.04895337
##
## $z0
## [1] 1.296654
##
## $lnL
## [1] -72.64896
##
## $method
## [1] "L-BFGS-B"
##
## $k
## [1] 3
##
## $aic
## [1] 151.2979
##
## $aicc
## [1] 151.7979
fitEB$opt
## $a
## [1] -1e-06
##
## $sigsq
## [1] 0.04096046
##
## $z0
## [1] 1.335361
##
## $lnL
## [1] -72.97717
##
## $method
## [1] "L-BFGS-B"
##
## $k
## [1] 3
##
## $aic
## [1] 151.9543
##
## $aicc
## [1] 152.4543
aic.vals<-setNames(c(fitBM$opt$aicc,fitOU$opt$aicc,fitEB$opt$aicc),
c("BM","OU","EB"))
aic.vals
## BM OU EB
## 150.1991 151.7979 152.4543
aic.w(aic.vals)
## BM OU EB
## 0.5638843 0.2535236 0.1825921
fitBM$opt
## $sigsq
## [1] 0.05996723
##
## $z0
## [1] 0.007962384
##
## $lnL
## [1] -82.88939
##
## $method
## [1] "Brent"
##
## $k
## [1] 2
##
## $aic
## [1] 169.7788
##
## $aicc
## [1] 170.0237
fitOU$opt
## $alpha
## [1] 2.718282
##
## $sigsq
## [1] 4.804233
##
## $z0
## [1] 0.2278837
##
## $lnL
## [1] -70.56991
##
## $method
## [1] "L-BFGS-B"
##
## $k
## [1] 3
##
## $aic
## [1] 147.1398
##
## $aicc
## [1] 147.6398
fitEB$opt
## $a
## [1] -1e-06
##
## $sigsq
## [1] 0.0599706
##
## $z0
## [1] 0.007962912
##
## $lnL
## [1] -82.88959
##
## $method
## [1] "L-BFGS-B"
##
## $k
## [1] 3
##
## $aic
## [1] 171.7792
##
## $aicc
## [1] 172.2792
aic.vals<-setNames(c(fitBM$opt$aicc,fitOU$opt$aicc,fitEB$opt$aicc),
c("BM","OU","EB"))
aic.vals
## BM OU EB
## 170.0237 147.6398 172.2792
aic.w(aic.vals)
## BM OU EB
## 0.00001378 0.99998175 0.00000446
fitBM$opt
## $sigsq
## [1] 0.02698684
##
## $z0
## [1] 0.5005985
##
## $lnL
## [1] -62.12972
##
## $method
## [1] "Brent"
##
## $k
## [1] 2
##
## $aic
## [1] 128.2594
##
## $aicc
## [1] 128.5043
fitOU$opt
## $alpha
## [1] 0.003028001
##
## $sigsq
## [1] 0.0290781
##
## $z0
## [1] 0.5128266
##
## $lnL
## [1] -62.0485
##
## $method
## [1] "L-BFGS-B"
##
## $k
## [1] 3
##
## $aic
## [1] 130.097
##
## $aicc
## [1] 130.597
fitEB$opt
## $a
## [1] -1e-06
##
## $sigsq
## [1] 0.02698818
##
## $z0
## [1] 0.5005965
##
## $lnL
## [1] -62.12974
##
## $method
## [1] "L-BFGS-B"
##
## $k
## [1] 3
##
## $aic
## [1] 130.2595
##
## $aicc
## [1] 130.7595
aic.vals<-setNames(c(fitBM$opt$aicc,fitOU$opt$aicc,fitEB$opt$aicc),
c("BM","OU","EB"))
aic.vals
## BM OU EB
## 128.5043 130.5970 130.7595
aic.w(aic.vals)
## BM OU EB
## 0.5970005 0.2096809 0.1933187
fitBM$opt
## $sigsq
## [1] 0.04813505
##
## $z0
## [1] -0.1281526
##
## $lnL
## [1] -77.17491
##
## $method
## [1] "Brent"
##
## $k
## [1] 2
##
## $aic
## [1] 158.3498
##
## $aicc
## [1] 158.5947
fitOU$opt
## $alpha
## [1] 0.04565845
##
## $sigsq
## [1] 0.09045466
##
## $z0
## [1] -0.07190474
##
## $lnL
## [1] -68.75383
##
## $method
## [1] "L-BFGS-B"
##
## $k
## [1] 3
##
## $aic
## [1] 143.5077
##
## $aicc
## [1] 144.0077
fitEB$opt
## $a
## [1] -1e-06
##
## $sigsq
## [1] 0.04813773
##
## $z0
## [1] -0.1281523
##
## $lnL
## [1] -77.1751
##
## $method
## [1] "L-BFGS-B"
##
## $k
## [1] 3
##
## $aic
## [1] 160.3502
##
## $aicc
## [1] 160.8502
aic.vals<-setNames(c(fitBM$opt$aicc,fitOU$opt$aicc,fitEB$opt$aicc),
c("BM","OU","EB"))
aic.vals
## BM OU EB
## 158.5947 144.0077 160.8502
aic.w(aic.vals)
## BM OU EB
## 0.00067931 0.99910075 0.00021994
dat<-setNames(trait$ePLA2,rownames(trait))
fitBM<-fitContinuous(tree,dat)
fitOU<-fitContinuous(tree,dat,model="OU")
fitEB<-fitContinuous(tree,dat,model="EB")
fitBM$opt
## $sigsq
## [1] 0.01783931
##
## $z0
## [1] 0.00254227
##
## $lnL
## [1] -51.36715
##
## $method
## [1] "Brent"
##
## $k
## [1] 2
##
## $aic
## [1] 106.7343
##
## $aicc
## [1] 106.9792
fitOU$opt
## $alpha
## [1] 0.003905488
##
## $sigsq
## [1] 0.01966365
##
## $z0
## [1] 0.01119636
##
## $lnL
## [1] -51.3004
##
## $method
## [1] "L-BFGS-B"
##
## $k
## [1] 3
##
## $aic
## [1] 108.6008
##
## $aicc
## [1] 109.1008
fitEB$opt
## $a
## [1] -1e-06
##
## $sigsq
## [1] 0.01784019
##
## $z0
## [1] 0.002541179
##
## $lnL
## [1] -51.36717
##
## $method
## [1] "L-BFGS-B"
##
## $k
## [1] 3
##
## $aic
## [1] 108.7343
##
## $aicc
## [1] 109.2343
aic.vals<-setNames(c(fitBM$opt$aicc,fitOU$opt$aicc,fitEB$opt$aicc),
c("BM","OU","EB"))
aic.vals
## BM OU EB
## 106.9792 109.1008 109.2343
aic.w(aic.vals)
## BM OU EB
## 0.5988027 0.2072932 0.1939041
tree<-read.nexus("./data/Final_tree.nex")
dat<-read.csv("./data/Ouwie_data/BPP_OUwie_ManyOptions_optima.csv",row.names = 1)
Make simmap tree for selective regime. We classified selective regime based on the phylomorphospace obtained from Barua and Mikheyev 2019. Figure below shows which snakes were clustered into which regime.
ad_reg<-setNames(dat[,2],rownames(dat))
simmap.tre<-make.simmap(tree, ad_reg, model = "ER")
## make.simmap is sampling character histories conditioned on the transition matrix
##
## Q =
## 1 2 3 4 5
## 1 -0.015510466 0.002585078 0.002585078 0.002585078 0.002585078
## 2 0.002585078 -0.015510466 0.002585078 0.002585078 0.002585078
## 3 0.002585078 0.002585078 -0.015510466 0.002585078 0.002585078
## 4 0.002585078 0.002585078 0.002585078 -0.015510466 0.002585078
## 5 0.002585078 0.002585078 0.002585078 0.002585078 -0.015510466
## 6 0.002585078 0.002585078 0.002585078 0.002585078 0.002585078
## 7 0.002585078 0.002585078 0.002585078 0.002585078 0.002585078
## 6 7
## 1 0.002585078 0.002585078
## 2 0.002585078 0.002585078
## 3 0.002585078 0.002585078
## 4 0.002585078 0.002585078
## 5 0.002585078 0.002585078
## 6 -0.015510466 0.002585078
## 7 0.002585078 -0.015510466
## (estimated using likelihood);
## and (mean) root node prior probabilities
## pi =
## 1 2 3 4 5 6 7
## 0.1428571 0.1428571 0.1428571 0.1428571 0.1428571 0.1428571 0.1428571
## Done.
plot(simmap.tre,type="fan",fsize=0.5,ftype="i")
## no colors provided. using the following legend:
## 1 2 3 4 5 6 7
## "black" "red" "green3" "blue" "cyan" "magenta" "yellow"
dat<-read.csv("./data/Ouwie_data/SVSP_OUwie_ManyOptions_optima.csv")
BM1_SVSP<-OUwie(phy = simmap.tre,data = dat,model="BM1",simmap.tree=TRUE,diagn = T)
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
BM1_SVSP
##
## Fit
## lnL AIC AICc BIC model ntax
## -77.13118 158.2624 158.5073 162.1649 BM1 52
##
## Rates
## -0.028433826 -0.065786707 -0.065788923 -0.091682733 -0.196308172
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.254442424 -0.259222055 -0.26328121 -0.272798588 -0.284773794
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.323558544 -0.327981232 -0.335892953 -0.351479006 -0.359161832
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.380235729 -0.399213836 -0.399284019 -0.4527582 -0.453846945
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.454790159 -0.463327573 -0.463654083 -0.473209269 -0.478528704
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.478787643 -0.505966472 -0.576323477 -0.599651816 -0.612242656
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.699934584 0.02381373 0.063071096 0.068901152 0.093272473
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 0.095307031 0.222783197 0.297477307 0.378206741 0.549678091
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 1.11791987 1.13186312 1.174566834 1.199064792 1.301684098
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 1.30629117 1.79412254 2.149960947 2.268008945 2.538965324
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 2.604500193 2.842844084 inode3122 inode3123 inode3151
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3159 inode3160 inode3162 inode3217 inode3218 inode3219
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3238 inode3239 inode3241 inode3242 inode3246 inode3259
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3264 inode3269 inode3272 inode3274 inode3279 inode3280
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3282 inode3284 inode3288 inode3290 inode3297 inode3301
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3315 inode3316 inode3319 inode3326 inode3351 inode3490
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3495 inode3496 inode3501 inode3502 inode3509 inode3513
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3514 inode3525 inode3538 inode3542 inode3572 inode3631
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3714 inode3732 inode3769 inode3970 inode4032 inode4086
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##
## Optima
## -0.028433826 -0.065786707 -0.065788923 -0.091682733 -0.196308172
## estimate 4.0576335 0 0 0 0
## se 0.7261147 0 0 0 0
## -0.254442424 -0.259222055 -0.26328121 -0.272798588 -0.284773794
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.323558544 -0.327981232 -0.335892953 -0.351479006 -0.359161832
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.380235729 -0.399213836 -0.399284019 -0.4527582 -0.453846945
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.454790159 -0.463327573 -0.463654083 -0.473209269 -0.478528704
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.478787643 -0.505966472 -0.576323477 -0.599651816 -0.612242656
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.699934584 0.02381373 0.063071096 0.068901152 0.093272473
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 0.095307031 0.222783197 0.297477307 0.378206741 0.549678091
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 1.11791987 1.13186312 1.174566834 1.199064792 1.301684098
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 1.30629117 1.79412254 2.149960947 2.268008945 2.538965324
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 2.604500193 2.842844084 inode3122 inode3123 inode3151 inode3159
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 0 0 0 0 0
## se 0 0 0 0 0
##
## Arrived at a reliable solution
OU1_SVSP<-OUwie(phy = simmap.tre, data = dat, model="OU1", simmap.tree=T,diagn = T)
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
OU1_SVSP
##
## Fit
## lnL AIC AICc BIC model ntax
## -77.13118 160.2624 160.7624 166.1161 OU1 52
##
## Rates
## -0.028433826 -0.065786707 -0.065788923 -0.091682733 -0.196308172
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.254442424 -0.259222055 -0.26328121 -0.272798588 -0.284773794
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.323558544 -0.327981232 -0.335892953 -0.351479006 -0.359161832
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.380235729 -0.399213836 -0.399284019 -0.4527582 -0.453846945
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.454790159 -0.463327573 -0.463654083 -0.473209269 -0.478528704
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.478787643 -0.505966472 -0.576323477 -0.599651816 -0.612242656
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.699934584 0.02381373 0.063071096 0.068901152 0.093272473
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## 0.095307031 0.222783197 0.297477307 0.378206741 0.549678091
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## 1.11791987 1.13186312 1.174566834 1.199064792 1.301684098
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## 1.30629117 1.79412254 2.149960947 2.268008945 2.538965324
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## 2.604500193 2.842844084 inode3122 inode3123 inode3151
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3159 inode3160 inode3162 inode3217 inode3218
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3219 inode3238 inode3239 inode3241 inode3242
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3246 inode3259 inode3264 inode3269 inode3272
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3274 inode3279 inode3280 inode3282 inode3284
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3288 inode3290 inode3297 inode3301 inode3315
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3316 inode3319 inode3326 inode3351 inode3490
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3495 inode3496 inode3501 inode3502 inode3509
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3513 inode3514 inode3525 inode3538 inode3542
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3572 inode3631 inode3714 inode3732 inode3769
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3970 inode4032 inode4086
## alpha 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02
##
##
## Optima
## -0.028433826 -0.065786707 -0.065788923 -0.091682733 -0.196308172
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.254442424 -0.259222055 -0.26328121 -0.272798588 -0.284773794
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.323558544 -0.327981232 -0.335892953 -0.351479006 -0.359161832
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.380235729 -0.399213836 -0.399284019 -0.4527582 -0.453846945
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.454790159 -0.463327573 -0.463654083 -0.473209269 -0.478528704
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.478787643 -0.505966472 -0.576323477 -0.599651816 -0.612242656
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.699934584 0.02381373 0.063071096 0.068901152 0.093272473
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 0.095307031 0.222783197 0.297477307 0.378206741 0.549678091
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 1.11791987 1.13186312 1.174566834 1.199064792 1.301684098
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 1.30629117 1.79412254 2.149960947 2.268008945 2.538965324
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 2.604500193 2.842844084 inode3122 inode3123 inode3151 inode3159
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##
##
## Half life (another way of reporting alpha)
## -0.028433826 -0.065786707 -0.065788923 -0.091682733 -0.196308172
## 308643937 308643937 308643937 308643937 308643937
## -0.254442424 -0.259222055 -0.26328121 -0.272798588 -0.284773794
## 308643937 308643937 308643937 308643937 308643937
## -0.323558544 -0.327981232 -0.335892953 -0.351479006 -0.359161832
## 308643937 308643937 308643937 308643937 308643937
## -0.380235729 -0.399213836 -0.399284019 -0.4527582 -0.453846945
## 308643937 308643937 308643937 308643937 308643937
## -0.454790159 -0.463327573 -0.463654083 -0.473209269 -0.478528704
## 308643937 308643937 308643937 308643937 308643937
## -0.478787643 -0.505966472 -0.576323477 -0.599651816 -0.612242656
## 308643937 308643937 308643937 308643937 308643937
## -0.699934584 0.02381373 0.063071096 0.068901152 0.093272473
## 308643937 308643937 308643937 308643937 308643937
## 0.095307031 0.222783197 0.297477307 0.378206741 0.549678091
## 308643937 308643937 308643937 308643937 308643937
## 1.11791987 1.13186312 1.174566834 1.199064792 1.301684098
## 308643937 308643937 308643937 308643937 308643937
## 1.30629117 1.79412254 2.149960947 2.268008945 2.538965324
## 308643937 308643937 308643937 308643937 308643937
## 2.604500193 2.842844084 inode3122 inode3123 inode3151
## 308643937 308643937 308643937 308643937 308643937
## inode3159 inode3160 inode3162 inode3217 inode3218
## 308643937 308643937 308643937 308643937 308643937
## inode3219 inode3238 inode3239 inode3241 inode3242
## 308643937 308643937 308643937 308643937 308643937
## inode3246 inode3259 inode3264 inode3269 inode3272
## 308643937 308643937 308643937 308643937 308643937
## inode3274 inode3279 inode3280 inode3282 inode3284
## 308643937 308643937 308643937 308643937 308643937
## inode3288 inode3290 inode3297 inode3301 inode3315
## 308643937 308643937 308643937 308643937 308643937
## inode3316 inode3319 inode3326 inode3351 inode3490
## 308643937 308643937 308643937 308643937 308643937
## inode3495 inode3496 inode3501 inode3502 inode3509
## 308643937 308643937 308643937 308643937 308643937
## inode3513 inode3514 inode3525 inode3538 inode3542
## 308643937 308643937 308643937 308643937 308643937
## inode3572 inode3631 inode3714 inode3732 inode3769
## 308643937 308643937 308643937 308643937 308643937
## inode3970 inode4032 inode4086
## 308643937 308643937 308643937
##
## Arrived at a reliable solution
OU1_SVSP$eigval
## [1] 2.6e+01 1.3e-06
OU1_SVSP$solution.se
## -0.028433826 -0.065786707 -0.065788923 -0.091682733 -0.196308172
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.254442424 -0.259222055 -0.26328121 -0.272798588 -0.284773794
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.323558544 -0.327981232 -0.335892953 -0.351479006 -0.359161832
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.380235729 -0.399213836 -0.399284019 -0.4527582 -0.453846945
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.454790159 -0.463327573 -0.463654083 -0.473209269 -0.478528704
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.478787643 -0.505966472 -0.576323477 -0.599651816 -0.612242656
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.699934584 0.02381373 0.063071096 0.068901152 0.093272473
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## 0.095307031 0.222783197 0.297477307 0.378206741 0.549678091
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## 1.11791987 1.13186312 1.174566834 1.199064792 1.301684098
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## 1.30629117 1.79412254 2.149960947 2.268008945 2.538965324
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## 2.604500193 2.842844084 inode3122 inode3123 inode3151
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3159 inode3160 inode3162 inode3217 inode3218
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3219 inode3238 inode3239 inode3241 inode3242
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3246 inode3259 inode3264 inode3269 inode3272
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3274 inode3279 inode3280 inode3282 inode3284
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3288 inode3290 inode3297 inode3301 inode3315
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3316 inode3319 inode3326 inode3351 inode3490
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3495 inode3496 inode3501 inode3502 inode3509
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3513 inode3514 inode3525 inode3538 inode3542
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3572 inode3631 inode3714 inode3732 inode3769
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3970 inode4032 inode4086
## alpha 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103
OUM_SVSP<-OUwie(phy = simmap.tre, data = dat, model="OUM", simmap.tree=T,diagn = T)
## Warning: You might not have enough data to fit this model well
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
OUM_SVSP
##
## Fit
## lnL AIC AICc BIC model ntax
## 85.24088 -152.4818 -148.196 -134.9206 OUM 52
##
##
## Rates
## 1 2 3 4 5 6
## alpha 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949
## sigma.sq 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326
## 7
## alpha 5.78373949
## sigma.sq 0.02552326
##
## Optima
## 1 2 3 4 5 6
## estimate 0.98278962 1.99999991 3.00016183 3.94380311 4.98768103 6.00000000
## se 0.03331039 0.04697305 0.01001451 0.02575421 0.01410894 0.03321496
## 7
## estimate 6.99998674
## se 0.01485411
##
##
## Half life (another way of reporting alpha)
## 1 2 3 4 5 6 7
## 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441
##
## Arrived at a reliable solution
aic<-setNames(c(BM1_SVSP$AICc,OU1_SVSP$AICc,OUM_SVSP$AICc),
c("BM","OU1","OUM"))
aic
## BM OU1 OUM
## 158.5073 160.7624 -148.1960
aic.w(aic)
## BM OU1 OUM
## 0 0 1
dat<-read.csv("./data/Ouwie_data/TFTx_OUwie_ManyOptions_optima.csv")
BM1_TFTx<-OUwie(phy = simmap.tre,data = dat,model="BM1",simmap.tree=TRUE,diagn = T)
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
BM1_TFTx
##
## Fit
## lnL AIC AICc BIC model ntax
## -77.13118 158.2624 158.5073 162.1649 BM1 52
##
## Rates
## -0.140629497 -0.151281523 -0.339477428 -0.343935613 -0.351900922
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.363737891 -0.36429282 -0.421421201 -0.428224485 -0.449261397
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.460376482 -0.466734078 -0.467614451 -0.471887205 -0.473776068
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.478411682 -0.481264314 -0.492629779 -0.494906486 -0.52278517
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.523308863 -0.535408592 -0.539435104 -0.542252225 -0.543732229
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.555961591 -0.569277353 -0.581015956 -0.589669336 -0.632877207
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.657107195 -0.665162495 -0.709372748 -0.731309262 -0.827893652
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.96572225 0.73567568 0.739710541 1.123078765 1.340010728
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 1.804132426 2.419250025 2.421919481 2.58619344 2.662975226
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 2.722817222 2.742528187 2.750632477 2.807834797 2.839970361
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 2.844393257 2.845816956 inode3122 inode3123 inode3151
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3159 inode3160 inode3162 inode3217 inode3218 inode3219
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3238 inode3239 inode3241 inode3242 inode3246 inode3259
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3264 inode3269 inode3272 inode3274 inode3279 inode3280
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3282 inode3284 inode3288 inode3290 inode3297 inode3301
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3315 inode3316 inode3319 inode3326 inode3351 inode3490
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3495 inode3496 inode3501 inode3502 inode3509 inode3513
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3514 inode3525 inode3538 inode3542 inode3572 inode3631
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3714 inode3732 inode3769 inode3970 inode4032 inode4086
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##
## Optima
## -0.140629497 -0.151281523 -0.339477428 -0.343935613 -0.351900922
## estimate 4.0576335 0 0 0 0
## se 0.7261147 0 0 0 0
## -0.363737891 -0.36429282 -0.421421201 -0.428224485 -0.449261397
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.460376482 -0.466734078 -0.467614451 -0.471887205 -0.473776068
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.478411682 -0.481264314 -0.492629779 -0.494906486 -0.52278517
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.523308863 -0.535408592 -0.539435104 -0.542252225 -0.543732229
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.555961591 -0.569277353 -0.581015956 -0.589669336 -0.632877207
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.657107195 -0.665162495 -0.709372748 -0.731309262 -0.827893652
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.96572225 0.73567568 0.739710541 1.123078765 1.340010728
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 1.804132426 2.419250025 2.421919481 2.58619344 2.662975226
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 2.722817222 2.742528187 2.750632477 2.807834797 2.839970361
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 2.844393257 2.845816956 inode3122 inode3123 inode3151 inode3159
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 0 0 0 0 0
## se 0 0 0 0 0
##
## Arrived at a reliable solution
OU1_TFTx<-OUwie(phy = simmap.tre, data = dat, model="OU1", simmap.tree=T,diagn = T)
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
OU1_TFTx
##
## Fit
## lnL AIC AICc BIC model ntax
## -77.13118 160.2624 160.7624 166.1161 OU1 52
##
## Rates
## -0.140629497 -0.151281523 -0.339477428 -0.343935613 -0.351900922
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.363737891 -0.36429282 -0.421421201 -0.428224485 -0.449261397
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.460376482 -0.466734078 -0.467614451 -0.471887205 -0.473776068
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.478411682 -0.481264314 -0.492629779 -0.494906486 -0.52278517
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.523308863 -0.535408592 -0.539435104 -0.542252225 -0.543732229
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.555961591 -0.569277353 -0.581015956 -0.589669336 -0.632877207
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.657107195 -0.665162495 -0.709372748 -0.731309262 -0.827893652
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.96572225 0.73567568 0.739710541 1.123078765 1.340010728
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## 1.804132426 2.419250025 2.421919481 2.58619344 2.662975226
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## 2.722817222 2.742528187 2.750632477 2.807834797 2.839970361
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## 2.844393257 2.845816956 inode3122 inode3123 inode3151
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3159 inode3160 inode3162 inode3217 inode3218
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3219 inode3238 inode3239 inode3241 inode3242
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3246 inode3259 inode3264 inode3269 inode3272
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3274 inode3279 inode3280 inode3282 inode3284
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3288 inode3290 inode3297 inode3301 inode3315
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3316 inode3319 inode3326 inode3351 inode3490
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3495 inode3496 inode3501 inode3502 inode3509
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3513 inode3514 inode3525 inode3538 inode3542
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3572 inode3631 inode3714 inode3732 inode3769
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3970 inode4032 inode4086
## alpha 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02
##
##
## Optima
## -0.140629497 -0.151281523 -0.339477428 -0.343935613 -0.351900922
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.363737891 -0.36429282 -0.421421201 -0.428224485 -0.449261397
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.460376482 -0.466734078 -0.467614451 -0.471887205 -0.473776068
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.478411682 -0.481264314 -0.492629779 -0.494906486 -0.52278517
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.523308863 -0.535408592 -0.539435104 -0.542252225 -0.543732229
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.555961591 -0.569277353 -0.581015956 -0.589669336 -0.632877207
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.657107195 -0.665162495 -0.709372748 -0.731309262 -0.827893652
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.96572225 0.73567568 0.739710541 1.123078765 1.340010728
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 1.804132426 2.419250025 2.421919481 2.58619344 2.662975226
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 2.722817222 2.742528187 2.750632477 2.807834797 2.839970361
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 2.844393257 2.845816956 inode3122 inode3123 inode3151 inode3159
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##
##
## Half life (another way of reporting alpha)
## -0.140629497 -0.151281523 -0.339477428 -0.343935613 -0.351900922
## 308643937 308643937 308643937 308643937 308643937
## -0.363737891 -0.36429282 -0.421421201 -0.428224485 -0.449261397
## 308643937 308643937 308643937 308643937 308643937
## -0.460376482 -0.466734078 -0.467614451 -0.471887205 -0.473776068
## 308643937 308643937 308643937 308643937 308643937
## -0.478411682 -0.481264314 -0.492629779 -0.494906486 -0.52278517
## 308643937 308643937 308643937 308643937 308643937
## -0.523308863 -0.535408592 -0.539435104 -0.542252225 -0.543732229
## 308643937 308643937 308643937 308643937 308643937
## -0.555961591 -0.569277353 -0.581015956 -0.589669336 -0.632877207
## 308643937 308643937 308643937 308643937 308643937
## -0.657107195 -0.665162495 -0.709372748 -0.731309262 -0.827893652
## 308643937 308643937 308643937 308643937 308643937
## -0.96572225 0.73567568 0.739710541 1.123078765 1.340010728
## 308643937 308643937 308643937 308643937 308643937
## 1.804132426 2.419250025 2.421919481 2.58619344 2.662975226
## 308643937 308643937 308643937 308643937 308643937
## 2.722817222 2.742528187 2.750632477 2.807834797 2.839970361
## 308643937 308643937 308643937 308643937 308643937
## 2.844393257 2.845816956 inode3122 inode3123 inode3151
## 308643937 308643937 308643937 308643937 308643937
## inode3159 inode3160 inode3162 inode3217 inode3218
## 308643937 308643937 308643937 308643937 308643937
## inode3219 inode3238 inode3239 inode3241 inode3242
## 308643937 308643937 308643937 308643937 308643937
## inode3246 inode3259 inode3264 inode3269 inode3272
## 308643937 308643937 308643937 308643937 308643937
## inode3274 inode3279 inode3280 inode3282 inode3284
## 308643937 308643937 308643937 308643937 308643937
## inode3288 inode3290 inode3297 inode3301 inode3315
## 308643937 308643937 308643937 308643937 308643937
## inode3316 inode3319 inode3326 inode3351 inode3490
## 308643937 308643937 308643937 308643937 308643937
## inode3495 inode3496 inode3501 inode3502 inode3509
## 308643937 308643937 308643937 308643937 308643937
## inode3513 inode3514 inode3525 inode3538 inode3542
## 308643937 308643937 308643937 308643937 308643937
## inode3572 inode3631 inode3714 inode3732 inode3769
## 308643937 308643937 308643937 308643937 308643937
## inode3970 inode4032 inode4086
## 308643937 308643937 308643937
##
## Arrived at a reliable solution
OU1_TFTx$eigval
## [1] 2.6e+01 1.3e-06
OU1_TFTx$solution.se
## -0.140629497 -0.151281523 -0.339477428 -0.343935613 -0.351900922
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.363737891 -0.36429282 -0.421421201 -0.428224485 -0.449261397
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.460376482 -0.466734078 -0.467614451 -0.471887205 -0.473776068
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.478411682 -0.481264314 -0.492629779 -0.494906486 -0.52278517
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.523308863 -0.535408592 -0.539435104 -0.542252225 -0.543732229
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.555961591 -0.569277353 -0.581015956 -0.589669336 -0.632877207
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.657107195 -0.665162495 -0.709372748 -0.731309262 -0.827893652
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.96572225 0.73567568 0.739710541 1.123078765 1.340010728
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## 1.804132426 2.419250025 2.421919481 2.58619344 2.662975226
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## 2.722817222 2.742528187 2.750632477 2.807834797 2.839970361
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## 2.844393257 2.845816956 inode3122 inode3123 inode3151
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3159 inode3160 inode3162 inode3217 inode3218
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3219 inode3238 inode3239 inode3241 inode3242
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3246 inode3259 inode3264 inode3269 inode3272
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3274 inode3279 inode3280 inode3282 inode3284
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3288 inode3290 inode3297 inode3301 inode3315
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3316 inode3319 inode3326 inode3351 inode3490
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3495 inode3496 inode3501 inode3502 inode3509
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3513 inode3514 inode3525 inode3538 inode3542
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3572 inode3631 inode3714 inode3732 inode3769
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3970 inode4032 inode4086
## alpha 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103
OUM_TFTx<-OUwie(phy = simmap.tre, data = dat, model="OUM", simmap.tree=T,diagn = T)
## Warning: You might not have enough data to fit this model well
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
OUM_TFTx
##
## Fit
## lnL AIC AICc BIC model ntax
## 85.24088 -152.4818 -148.196 -134.9206 OUM 52
##
##
## Rates
## 1 2 3 4 5 6
## alpha 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949
## sigma.sq 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326
## 7
## alpha 5.78373949
## sigma.sq 0.02552326
##
## Optima
## 1 2 3 4 5 6
## estimate 0.98278962 1.99999991 3.00016183 3.94380311 4.98768103 6.00000000
## se 0.03331039 0.04697305 0.01001451 0.02575421 0.01410894 0.03321496
## 7
## estimate 6.99998674
## se 0.01485411
##
##
## Half life (another way of reporting alpha)
## 1 2 3 4 5 6 7
## 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441
##
## Arrived at a reliable solution
aic<-setNames(c(BM1_TFTx$AICc,OU1_TFTx$AICc,OUM_TFTx$AICc),
c("BM","OU1","OUM"))
aic
## BM OU1 OUM
## 158.5073 160.7624 -148.1960
aic.w(aic)
## BM OU1 OUM
## 0 0 1
dat<-read.csv("./data/Ouwie_data/SVMP_OUwie_ManyOptions_optima.csv")
BM1_SVMP<-OUwie(phy = simmap.tre,data = dat,model="BM1",simmap.tree=TRUE,diagn = T)
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
BM1_SVMP
##
## Fit
## lnL AIC AICc BIC model ntax
## -93.44696 190.8939 191.1388 194.7964 BM1 52
##
## Rates
## -0.028600184 -0.160843603 -0.235324367 -0.314729465 -0.331612132
## alpha NA NA NA NA NA
## sigma.sq 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418
## -0.334277933 -0.336945636 -0.337468929 -0.399213836 -0.399284019
## alpha NA NA NA NA NA
## sigma.sq 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418
## -0.4034999 -0.454790159 -0.483120435 -0.498780177 -0.508750647
## alpha NA NA NA NA NA
## sigma.sq 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418
## -0.556403047 -0.563339519 -0.612242656 0.24612442 0.688226777
## alpha NA NA NA NA NA
## sigma.sq 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418
## 0.716248171 0.800457806 0.852053529 0.884429117 1.105054626
## alpha NA NA NA NA NA
## sigma.sq 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418
## 1.501471811 1.730054146 1.739986761 1.938191918 2.055614142
## alpha NA NA NA NA NA
## sigma.sq 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418
## 2.13114086 2.347170187 2.350545516 2.38904884 2.485664868
## alpha NA NA NA NA NA
## sigma.sq 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418
## 2.505774697 2.566762637 2.574411326 2.706669156 2.712007513
## alpha NA NA NA NA NA
## sigma.sq 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418
## 2.722965014 2.732313956 2.73286191 2.751484952 2.753080674
## alpha NA NA NA NA NA
## sigma.sq 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418
## 2.760067398 2.774368128 2.795360528 2.803163813 2.806058383
## alpha NA NA NA NA NA
## sigma.sq 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418
## 2.821722852 2.840055323 inode3122 inode3123 inode3151
## alpha NA NA NA NA NA
## sigma.sq 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418
## inode3159 inode3160 inode3162 inode3217 inode3218 inode3219
## alpha NA NA NA NA NA NA
## sigma.sq 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418
## inode3238 inode3239 inode3241 inode3242 inode3246 inode3259
## alpha NA NA NA NA NA NA
## sigma.sq 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418
## inode3264 inode3269 inode3272 inode3274 inode3279 inode3280
## alpha NA NA NA NA NA NA
## sigma.sq 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418
## inode3282 inode3284 inode3288 inode3290 inode3297 inode3301
## alpha NA NA NA NA NA NA
## sigma.sq 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418
## inode3315 inode3316 inode3319 inode3326 inode3351 inode3490
## alpha NA NA NA NA NA NA
## sigma.sq 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418
## inode3495 inode3496 inode3501 inode3502 inode3509 inode3513
## alpha NA NA NA NA NA NA
## sigma.sq 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418
## inode3514 inode3525 inode3538 inode3542 inode3572 inode3631
## alpha NA NA NA NA NA NA
## sigma.sq 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418
## inode3714 inode3732 inode3769 inode3970 inode4032 inode4086
## alpha NA NA NA NA NA NA
## sigma.sq 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418 0.09001418
##
## Optima
## -0.028600184 -0.160843603 -0.235324367 -0.314729465 -0.331612132
## estimate 2.3849719 0 0 0 0
## se 0.9937374 0 0 0 0
## -0.334277933 -0.336945636 -0.337468929 -0.399213836 -0.399284019
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.4034999 -0.454790159 -0.483120435 -0.498780177 -0.508750647
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.556403047 -0.563339519 -0.612242656 0.24612442 0.688226777
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 0.716248171 0.800457806 0.852053529 0.884429117 1.105054626
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 1.501471811 1.730054146 1.739986761 1.938191918 2.055614142
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 2.13114086 2.347170187 2.350545516 2.38904884 2.485664868
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 2.505774697 2.566762637 2.574411326 2.706669156 2.712007513
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 2.722965014 2.732313956 2.73286191 2.751484952 2.753080674
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 2.760067398 2.774368128 2.795360528 2.803163813 2.806058383
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 2.821722852 2.840055323 inode3122 inode3123 inode3151 inode3159
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 0 0 0 0 0
## se 0 0 0 0 0
##
## Arrived at a reliable solution
OU1_SVMP<-OUwie(phy = simmap.tre, data = dat, model="OU1", simmap.tree=T,diagn = T)
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
## Warning in sqrt(diag(pseudoinverse(h))): NaNs produced
OU1_SVMP
##
## Fit
## lnL AIC AICc BIC model ntax
## -93.44696 192.8939 193.3939 198.7477 OU1 52
##
## Rates
## -0.028600184 -0.160843603 -0.235324367 -0.314729465 -0.331612132
## alpha 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
## -0.334277933 -0.336945636 -0.337468929 -0.399213836 -0.399284019
## alpha 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
## -0.4034999 -0.454790159 -0.483120435 -0.498780177 -0.508750647
## alpha 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
## -0.556403047 -0.563339519 -0.612242656 0.24612442 0.688226777
## alpha 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
## 0.716248171 0.800457806 0.852053529 0.884429117 1.105054626
## alpha 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
## 1.501471811 1.730054146 1.739986761 1.938191918 2.055614142
## alpha 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
## 2.13114086 2.347170187 2.350545516 2.38904884 2.485664868
## alpha 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
## 2.505774697 2.566762637 2.574411326 2.706669156 2.712007513
## alpha 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
## 2.722965014 2.732313956 2.73286191 2.751484952 2.753080674
## alpha 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
## 2.760067398 2.774368128 2.795360528 2.803163813 2.806058383
## alpha 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
## 2.821722852 2.840055323 inode3122 inode3123 inode3151
## alpha 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
## inode3159 inode3160 inode3162 inode3217 inode3218
## alpha 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
## inode3219 inode3238 inode3239 inode3241 inode3242
## alpha 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
## inode3246 inode3259 inode3264 inode3269 inode3272
## alpha 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
## inode3274 inode3279 inode3280 inode3282 inode3284
## alpha 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
## inode3288 inode3290 inode3297 inode3301 inode3315
## alpha 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
## inode3316 inode3319 inode3326 inode3351 inode3490
## alpha 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
## inode3495 inode3496 inode3501 inode3502 inode3509
## alpha 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
## inode3513 inode3514 inode3525 inode3538 inode3542
## alpha 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
## inode3572 inode3631 inode3714 inode3732 inode3769
## alpha 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02 9.000553e-02
## inode3970 inode4032 inode4086
## alpha 2.061154e-09 2.061154e-09 2.061154e-09
## sigma.sq 9.000553e-02 9.000553e-02 9.000553e-02
##
##
## Optima
## -0.028600184 -0.160843603 -0.235324367 -0.314729465 -0.331612132
## estimate 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719
## se 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895
## -0.334277933 -0.336945636 -0.337468929 -0.399213836 -0.399284019
## estimate 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719
## se 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895
## -0.4034999 -0.454790159 -0.483120435 -0.498780177 -0.508750647
## estimate 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719
## se 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895
## -0.556403047 -0.563339519 -0.612242656 0.24612442 0.688226777
## estimate 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719
## se 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895
## 0.716248171 0.800457806 0.852053529 0.884429117 1.105054626
## estimate 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719
## se 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895
## 1.501471811 1.730054146 1.739986761 1.938191918 2.055614142
## estimate 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719
## se 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895
## 2.13114086 2.347170187 2.350545516 2.38904884 2.485664868
## estimate 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719
## se 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895
## 2.505774697 2.566762637 2.574411326 2.706669156 2.712007513
## estimate 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719
## se 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895
## 2.722965014 2.732313956 2.73286191 2.751484952 2.753080674
## estimate 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719
## se 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895
## 2.760067398 2.774368128 2.795360528 2.803163813 2.806058383
## estimate 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719
## se 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895
## 2.821722852 2.840055323 inode3122 inode3123 inode3151 inode3159
## estimate 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719
## se 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895
## inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719
## se 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895
## inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719
## se 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895
## inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719
## se 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895
## inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719
## se 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895
## inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719
## se 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895
## inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719
## se 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895
## inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719
## se 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895
## inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 2.3849719 2.3849719 2.3849719 2.3849719 2.3849719
## se 0.9936895 0.9936895 0.9936895 0.9936895 0.9936895
##
##
## Half life (another way of reporting alpha)
## -0.028600184 -0.160843603 -0.235324367 -0.314729465 -0.331612132
## 336290887 336290887 336290887 336290887 336290887
## -0.334277933 -0.336945636 -0.337468929 -0.399213836 -0.399284019
## 336290887 336290887 336290887 336290887 336290887
## -0.4034999 -0.454790159 -0.483120435 -0.498780177 -0.508750647
## 336290887 336290887 336290887 336290887 336290887
## -0.556403047 -0.563339519 -0.612242656 0.24612442 0.688226777
## 336290887 336290887 336290887 336290887 336290887
## 0.716248171 0.800457806 0.852053529 0.884429117 1.105054626
## 336290887 336290887 336290887 336290887 336290887
## 1.501471811 1.730054146 1.739986761 1.938191918 2.055614142
## 336290887 336290887 336290887 336290887 336290887
## 2.13114086 2.347170187 2.350545516 2.38904884 2.485664868
## 336290887 336290887 336290887 336290887 336290887
## 2.505774697 2.566762637 2.574411326 2.706669156 2.712007513
## 336290887 336290887 336290887 336290887 336290887
## 2.722965014 2.732313956 2.73286191 2.751484952 2.753080674
## 336290887 336290887 336290887 336290887 336290887
## 2.760067398 2.774368128 2.795360528 2.803163813 2.806058383
## 336290887 336290887 336290887 336290887 336290887
## 2.821722852 2.840055323 inode3122 inode3123 inode3151
## 336290887 336290887 336290887 336290887 336290887
## inode3159 inode3160 inode3162 inode3217 inode3218
## 336290887 336290887 336290887 336290887 336290887
## inode3219 inode3238 inode3239 inode3241 inode3242
## 336290887 336290887 336290887 336290887 336290887
## inode3246 inode3259 inode3264 inode3269 inode3272
## 336290887 336290887 336290887 336290887 336290887
## inode3274 inode3279 inode3280 inode3282 inode3284
## 336290887 336290887 336290887 336290887 336290887
## inode3288 inode3290 inode3297 inode3301 inode3315
## 336290887 336290887 336290887 336290887 336290887
## inode3316 inode3319 inode3326 inode3351 inode3490
## 336290887 336290887 336290887 336290887 336290887
## inode3495 inode3496 inode3501 inode3502 inode3509
## 336290887 336290887 336290887 336290887 336290887
## inode3513 inode3514 inode3525 inode3538 inode3542
## 336290887 336290887 336290887 336290887 336290887
## inode3572 inode3631 inode3714 inode3732 inode3769
## 336290887 336290887 336290887 336290887 336290887
## inode3970 inode4032 inode4086
## 336290887 336290887 336290887
##
## The objective function may be at a saddle point -- check eigenvectors or try a simpler model
OU1_SVMP$eigval
## [1] 2.6e+01 -1.3e-07
OU1_SVMP$solution.se
## -0.028600184 -0.160843603 -0.235324367 -0.314729465 -0.331612132
## alpha NaN NaN NaN NaN NaN
## sigma.sq 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173
## -0.334277933 -0.336945636 -0.337468929 -0.399213836 -0.399284019
## alpha NaN NaN NaN NaN NaN
## sigma.sq 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173
## -0.4034999 -0.454790159 -0.483120435 -0.498780177 -0.508750647
## alpha NaN NaN NaN NaN NaN
## sigma.sq 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173
## -0.556403047 -0.563339519 -0.612242656 0.24612442 0.688226777
## alpha NaN NaN NaN NaN NaN
## sigma.sq 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173
## 0.716248171 0.800457806 0.852053529 0.884429117 1.105054626
## alpha NaN NaN NaN NaN NaN
## sigma.sq 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173
## 1.501471811 1.730054146 1.739986761 1.938191918 2.055614142
## alpha NaN NaN NaN NaN NaN
## sigma.sq 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173
## 2.13114086 2.347170187 2.350545516 2.38904884 2.485664868
## alpha NaN NaN NaN NaN NaN
## sigma.sq 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173
## 2.505774697 2.566762637 2.574411326 2.706669156 2.712007513
## alpha NaN NaN NaN NaN NaN
## sigma.sq 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173
## 2.722965014 2.732313956 2.73286191 2.751484952 2.753080674
## alpha NaN NaN NaN NaN NaN
## sigma.sq 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173
## 2.760067398 2.774368128 2.795360528 2.803163813 2.806058383
## alpha NaN NaN NaN NaN NaN
## sigma.sq 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173
## 2.821722852 2.840055323 inode3122 inode3123 inode3151 inode3159
## alpha NaN NaN NaN NaN NaN NaN
## sigma.sq 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173
## inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## alpha NaN NaN NaN NaN NaN NaN
## sigma.sq 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173
## inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## alpha NaN NaN NaN NaN NaN NaN
## sigma.sq 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173
## inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## alpha NaN NaN NaN NaN NaN NaN
## sigma.sq 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173
## inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## alpha NaN NaN NaN NaN NaN NaN
## sigma.sq 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173
## inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## alpha NaN NaN NaN NaN NaN NaN
## sigma.sq 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173
## inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## alpha NaN NaN NaN NaN NaN NaN
## sigma.sq 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173
## inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## alpha NaN NaN NaN NaN NaN NaN
## sigma.sq 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173
## inode3732 inode3769 inode3970 inode4032 inode4086
## alpha NaN NaN NaN NaN NaN
## sigma.sq 0.1961173 0.1961173 0.1961173 0.1961173 0.1961173
OUM_SVMP<-OUwie(phy = simmap.tre, data = dat, model="OUM", simmap.tree=T,diagn = T)
## Warning: You might not have enough data to fit this model well
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
OUM_SVMP
##
## Fit
## lnL AIC AICc BIC model ntax
## -79.2955 176.591 180.8767 194.1522 OUM 52
##
##
## Rates
## 1 2 3 4 5 6
## alpha 0.2779875 0.2779875 0.2779875 0.2779875 0.2779875 0.2779875
## sigma.sq 0.6909299 0.6909299 0.6909299 0.6909299 0.6909299 0.6909299
## 7
## alpha 0.2779875
## sigma.sq 0.6909299
##
## Optima
## 1 2 3 4 5 6
## estimate 9.031596 2.315193 4.0468147 0.7470476 2.3892583 1.0004442
## se 1.954092 2.256422 0.2455787 2.2651647 0.3627398 0.8008283
## 7
## estimate -0.9307609
## se 0.3368008
##
##
## Half life (another way of reporting alpha)
## 1 2 3 4 5 6 7
## 2.493447 2.493447 2.493447 2.493447 2.493447 2.493447 2.493447
##
## Arrived at a reliable solution
aic<-setNames(c(BM1_SVMP$AICc,OU1_SVMP$AICc,OUM_SVMP$AICc),
c("BM","OU1","OUM"))
aic
## BM OU1 OUM
## 191.1388 193.3939 180.8767
aic.w(aic)
## BM OU1 OUM
## 0.00586446 0.00189906 0.99223648
dat<-read.csv("./data/Ouwie_data/vPLA2_OUwie_ManyOptions_optima.csv")
BM1_vPLA2<-OUwie(phy = simmap.tre,data = dat,model="BM1",simmap.tree=TRUE,diagn = T)
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
BM1_vPLA2
##
## Fit
## lnL AIC AICc BIC model ntax
## -77.13118 158.2624 158.5073 162.1649 BM1 52
##
## Rates
## -0.05037806 -0.05558464 -0.128998329 -0.19150365 -0.214161925
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.260215768 -0.273551879 -0.327981232 -0.334277933 -0.347029762
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.359161832 -0.364412135 -0.375611762 -0.380235729 -0.399213836
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.399284019 -0.408989879 -0.445499084 -0.454790159 -0.456943595
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.463327573 -0.463654083 -0.473209269 -0.483120435 -0.505966472
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.539435104 -0.563339519 -0.612216239 -0.612242656 -0.61894364
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.705954615 0.030183724 0.086301032 0.173260936 0.197482907
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 0.289149918 0.305865064 0.641462714 0.718516561 0.968893752
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 1.232175577 1.234150763 1.318284305 1.335952395 1.620250928
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 1.928659323 2.007079893 2.463355156 2.532379278 2.559969588
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 2.831003753 2.841994278 inode3122 inode3123 inode3151
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3159 inode3160 inode3162 inode3217 inode3218 inode3219
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3238 inode3239 inode3241 inode3242 inode3246 inode3259
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3264 inode3269 inode3272 inode3274 inode3279 inode3280
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3282 inode3284 inode3288 inode3290 inode3297 inode3301
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3315 inode3316 inode3319 inode3326 inode3351 inode3490
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3495 inode3496 inode3501 inode3502 inode3509 inode3513
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3514 inode3525 inode3538 inode3542 inode3572 inode3631
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3714 inode3732 inode3769 inode3970 inode4032 inode4086
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##
## Optima
## -0.05037806 -0.05558464 -0.128998329 -0.19150365 -0.214161925
## estimate 4.0576335 0 0 0 0
## se 0.7261147 0 0 0 0
## -0.260215768 -0.273551879 -0.327981232 -0.334277933 -0.347029762
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.359161832 -0.364412135 -0.375611762 -0.380235729 -0.399213836
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.399284019 -0.408989879 -0.445499084 -0.454790159 -0.456943595
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.463327573 -0.463654083 -0.473209269 -0.483120435 -0.505966472
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.539435104 -0.563339519 -0.612216239 -0.612242656 -0.61894364
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.705954615 0.030183724 0.086301032 0.173260936 0.197482907
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 0.289149918 0.305865064 0.641462714 0.718516561 0.968893752
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 1.232175577 1.234150763 1.318284305 1.335952395 1.620250928
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 1.928659323 2.007079893 2.463355156 2.532379278 2.559969588
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 2.831003753 2.841994278 inode3122 inode3123 inode3151 inode3159
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 0 0 0 0 0
## se 0 0 0 0 0
##
## Arrived at a reliable solution
OU1_vPLA2<-OUwie(phy = simmap.tre, data = dat, model="OU1", simmap.tree=T,diagn = T)
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
OU1_vPLA2
##
## Fit
## lnL AIC AICc BIC model ntax
## -77.13118 160.2624 160.7624 166.1161 OU1 52
##
## Rates
## -0.05037806 -0.05558464 -0.128998329 -0.19150365 -0.214161925
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.260215768 -0.273551879 -0.327981232 -0.334277933 -0.347029762
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.359161832 -0.364412135 -0.375611762 -0.380235729 -0.399213836
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.399284019 -0.408989879 -0.445499084 -0.454790159 -0.456943595
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.463327573 -0.463654083 -0.473209269 -0.483120435 -0.505966472
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.539435104 -0.563339519 -0.612216239 -0.612242656 -0.61894364
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.705954615 0.030183724 0.086301032 0.173260936 0.197482907
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## 0.289149918 0.305865064 0.641462714 0.718516561 0.968893752
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## 1.232175577 1.234150763 1.318284305 1.335952395 1.620250928
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## 1.928659323 2.007079893 2.463355156 2.532379278 2.559969588
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## 2.831003753 2.841994278 inode3122 inode3123 inode3151
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3159 inode3160 inode3162 inode3217 inode3218
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3219 inode3238 inode3239 inode3241 inode3242
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3246 inode3259 inode3264 inode3269 inode3272
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3274 inode3279 inode3280 inode3282 inode3284
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3288 inode3290 inode3297 inode3301 inode3315
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3316 inode3319 inode3326 inode3351 inode3490
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3495 inode3496 inode3501 inode3502 inode3509
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3513 inode3514 inode3525 inode3538 inode3542
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3572 inode3631 inode3714 inode3732 inode3769
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3970 inode4032 inode4086
## alpha 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02
##
##
## Optima
## -0.05037806 -0.05558464 -0.128998329 -0.19150365 -0.214161925
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.260215768 -0.273551879 -0.327981232 -0.334277933 -0.347029762
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.359161832 -0.364412135 -0.375611762 -0.380235729 -0.399213836
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.399284019 -0.408989879 -0.445499084 -0.454790159 -0.456943595
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.463327573 -0.463654083 -0.473209269 -0.483120435 -0.505966472
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.539435104 -0.563339519 -0.612216239 -0.612242656 -0.61894364
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.705954615 0.030183724 0.086301032 0.173260936 0.197482907
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 0.289149918 0.305865064 0.641462714 0.718516561 0.968893752
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 1.232175577 1.234150763 1.318284305 1.335952395 1.620250928
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 1.928659323 2.007079893 2.463355156 2.532379278 2.559969588
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 2.831003753 2.841994278 inode3122 inode3123 inode3151 inode3159
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##
##
## Half life (another way of reporting alpha)
## -0.05037806 -0.05558464 -0.128998329 -0.19150365 -0.214161925
## 308643937 308643937 308643937 308643937 308643937
## -0.260215768 -0.273551879 -0.327981232 -0.334277933 -0.347029762
## 308643937 308643937 308643937 308643937 308643937
## -0.359161832 -0.364412135 -0.375611762 -0.380235729 -0.399213836
## 308643937 308643937 308643937 308643937 308643937
## -0.399284019 -0.408989879 -0.445499084 -0.454790159 -0.456943595
## 308643937 308643937 308643937 308643937 308643937
## -0.463327573 -0.463654083 -0.473209269 -0.483120435 -0.505966472
## 308643937 308643937 308643937 308643937 308643937
## -0.539435104 -0.563339519 -0.612216239 -0.612242656 -0.61894364
## 308643937 308643937 308643937 308643937 308643937
## -0.705954615 0.030183724 0.086301032 0.173260936 0.197482907
## 308643937 308643937 308643937 308643937 308643937
## 0.289149918 0.305865064 0.641462714 0.718516561 0.968893752
## 308643937 308643937 308643937 308643937 308643937
## 1.232175577 1.234150763 1.318284305 1.335952395 1.620250928
## 308643937 308643937 308643937 308643937 308643937
## 1.928659323 2.007079893 2.463355156 2.532379278 2.559969588
## 308643937 308643937 308643937 308643937 308643937
## 2.831003753 2.841994278 inode3122 inode3123 inode3151
## 308643937 308643937 308643937 308643937 308643937
## inode3159 inode3160 inode3162 inode3217 inode3218
## 308643937 308643937 308643937 308643937 308643937
## inode3219 inode3238 inode3239 inode3241 inode3242
## 308643937 308643937 308643937 308643937 308643937
## inode3246 inode3259 inode3264 inode3269 inode3272
## 308643937 308643937 308643937 308643937 308643937
## inode3274 inode3279 inode3280 inode3282 inode3284
## 308643937 308643937 308643937 308643937 308643937
## inode3288 inode3290 inode3297 inode3301 inode3315
## 308643937 308643937 308643937 308643937 308643937
## inode3316 inode3319 inode3326 inode3351 inode3490
## 308643937 308643937 308643937 308643937 308643937
## inode3495 inode3496 inode3501 inode3502 inode3509
## 308643937 308643937 308643937 308643937 308643937
## inode3513 inode3514 inode3525 inode3538 inode3542
## 308643937 308643937 308643937 308643937 308643937
## inode3572 inode3631 inode3714 inode3732 inode3769
## 308643937 308643937 308643937 308643937 308643937
## inode3970 inode4032 inode4086
## 308643937 308643937 308643937
##
## Arrived at a reliable solution
OU1_vPLA2$eigval
## [1] 2.6e+01 1.3e-06
OU1_vPLA2$solution.se
## -0.05037806 -0.05558464 -0.128998329 -0.19150365 -0.214161925
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.260215768 -0.273551879 -0.327981232 -0.334277933 -0.347029762
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.359161832 -0.364412135 -0.375611762 -0.380235729 -0.399213836
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.399284019 -0.408989879 -0.445499084 -0.454790159 -0.456943595
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.463327573 -0.463654083 -0.473209269 -0.483120435 -0.505966472
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.539435104 -0.563339519 -0.612216239 -0.612242656 -0.61894364
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.705954615 0.030183724 0.086301032 0.173260936 0.197482907
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## 0.289149918 0.305865064 0.641462714 0.718516561 0.968893752
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## 1.232175577 1.234150763 1.318284305 1.335952395 1.620250928
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## 1.928659323 2.007079893 2.463355156 2.532379278 2.559969588
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## 2.831003753 2.841994278 inode3122 inode3123 inode3151
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3159 inode3160 inode3162 inode3217 inode3218
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3219 inode3238 inode3239 inode3241 inode3242
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3246 inode3259 inode3264 inode3269 inode3272
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3274 inode3279 inode3280 inode3282 inode3284
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3288 inode3290 inode3297 inode3301 inode3315
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3316 inode3319 inode3326 inode3351 inode3490
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3495 inode3496 inode3501 inode3502 inode3509
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3513 inode3514 inode3525 inode3538 inode3542
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3572 inode3631 inode3714 inode3732 inode3769
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3970 inode4032 inode4086
## alpha 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103
OUM_vPLA2<-OUwie(phy = simmap.tre, data = dat, model="OUM", simmap.tree=T,diagn = T)
## Warning: You might not have enough data to fit this model well
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
OUM_vPLA2
##
## Fit
## lnL AIC AICc BIC model ntax
## 85.24088 -152.4818 -148.196 -134.9206 OUM 52
##
##
## Rates
## 1 2 3 4 5 6
## alpha 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949
## sigma.sq 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326
## 7
## alpha 5.78373949
## sigma.sq 0.02552326
##
## Optima
## 1 2 3 4 5 6
## estimate 0.98278962 1.99999991 3.00016183 3.94380311 4.98768103 6.00000000
## se 0.03331039 0.04697305 0.01001451 0.02575421 0.01410894 0.03321496
## 7
## estimate 6.99998674
## se 0.01485411
##
##
## Half life (another way of reporting alpha)
## 1 2 3 4 5 6 7
## 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441
##
## Arrived at a reliable solution
aic<-setNames(c(BM1_vPLA2$AICc,OU1_vPLA2$AICc,OUM_vPLA2$AICc),
c("BM","OU1","OUM"))
aic
## BM OU1 OUM
## 158.5073 160.7624 -148.1960
aic.w(aic)
## BM OU1 OUM
## 0 0 1
dat<-read.csv("./data/Ouwie_data/ePLA2_OUwie_ManyOptions_optima.csv")
BM1_ePLA2<-OUwie(phy = simmap.tre,data = dat,model="BM1",simmap.tree=TRUE,diagn = T)
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
BM1_ePLA2
##
## Fit
## lnL AIC AICc BIC model ntax
## -77.13118 158.2624 158.5073 162.1649 BM1 52
##
## Rates
## -0.080031991 -0.177729566 -0.288225932 -0.325407223 -0.336320973
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.343935613 -0.347029762 -0.36429282 -0.422992017 -0.425565648
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.428224485 -0.449261397 -0.461474263 -0.463654083 -0.466734078
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.467614451 -0.478411682 -0.494906486 -0.496800054 -0.52278517
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.523308863 -0.527913521 -0.535408592 -0.539435104 -0.542252225
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.555961591 -0.569277353 -0.581015956 -0.581916282 -0.603132172
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.612216239 -0.632877207 -0.657107195 -0.665162495 -0.684832772
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.709372748 -0.731309262 -0.794196933 -0.827893652 -0.900691872
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.96572225 0.148517432 0.363798869 0.379063726 0.451182501
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 0.840437155 1.216401792 1.559973376 1.977427802 2.414894519
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 2.647357137 2.799948184 inode3122 inode3123 inode3151
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3159 inode3160 inode3162 inode3217 inode3218 inode3219
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3238 inode3239 inode3241 inode3242 inode3246 inode3259
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3264 inode3269 inode3272 inode3274 inode3279 inode3280
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3282 inode3284 inode3288 inode3290 inode3297 inode3301
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3315 inode3316 inode3319 inode3326 inode3351 inode3490
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3495 inode3496 inode3501 inode3502 inode3509 inode3513
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3514 inode3525 inode3538 inode3542 inode3572 inode3631
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3714 inode3732 inode3769 inode3970 inode4032 inode4086
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##
## Optima
## -0.080031991 -0.177729566 -0.288225932 -0.325407223 -0.336320973
## estimate 4.0576335 0 0 0 0
## se 0.7261147 0 0 0 0
## -0.343935613 -0.347029762 -0.36429282 -0.422992017 -0.425565648
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.428224485 -0.449261397 -0.461474263 -0.463654083 -0.466734078
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.467614451 -0.478411682 -0.494906486 -0.496800054 -0.52278517
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.523308863 -0.527913521 -0.535408592 -0.539435104 -0.542252225
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.555961591 -0.569277353 -0.581015956 -0.581916282 -0.603132172
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.612216239 -0.632877207 -0.657107195 -0.665162495 -0.684832772
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.709372748 -0.731309262 -0.794196933 -0.827893652 -0.900691872
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.96572225 0.148517432 0.363798869 0.379063726 0.451182501
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 0.840437155 1.216401792 1.559973376 1.977427802 2.414894519
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 2.647357137 2.799948184 inode3122 inode3123 inode3151 inode3159
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 0 0 0 0 0
## se 0 0 0 0 0
##
## Arrived at a reliable solution
OU1_ePLA2<-OUwie(phy = simmap.tre, data = dat, model="OU1", simmap.tree=T,diagn = T)
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
OU1_ePLA2
##
## Fit
## lnL AIC AICc BIC model ntax
## -77.13118 160.2624 160.7624 166.1161 OU1 52
##
## Rates
## -0.080031991 -0.177729566 -0.288225932 -0.325407223 -0.336320973
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.343935613 -0.347029762 -0.36429282 -0.422992017 -0.425565648
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.428224485 -0.449261397 -0.461474263 -0.463654083 -0.466734078
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.467614451 -0.478411682 -0.494906486 -0.496800054 -0.52278517
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.523308863 -0.527913521 -0.535408592 -0.539435104 -0.542252225
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.555961591 -0.569277353 -0.581015956 -0.581916282 -0.603132172
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.612216239 -0.632877207 -0.657107195 -0.665162495 -0.684832772
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.709372748 -0.731309262 -0.794196933 -0.827893652 -0.900691872
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.96572225 0.148517432 0.363798869 0.379063726 0.451182501
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## 0.840437155 1.216401792 1.559973376 1.977427802 2.414894519
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## 2.647357137 2.799948184 inode3122 inode3123 inode3151
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3159 inode3160 inode3162 inode3217 inode3218
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3219 inode3238 inode3239 inode3241 inode3242
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3246 inode3259 inode3264 inode3269 inode3272
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3274 inode3279 inode3280 inode3282 inode3284
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3288 inode3290 inode3297 inode3301 inode3315
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3316 inode3319 inode3326 inode3351 inode3490
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3495 inode3496 inode3501 inode3502 inode3509
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3513 inode3514 inode3525 inode3538 inode3542
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3572 inode3631 inode3714 inode3732 inode3769
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3970 inode4032 inode4086
## alpha 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02
##
##
## Optima
## -0.080031991 -0.177729566 -0.288225932 -0.325407223 -0.336320973
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.343935613 -0.347029762 -0.36429282 -0.422992017 -0.425565648
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.428224485 -0.449261397 -0.461474263 -0.463654083 -0.466734078
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.467614451 -0.478411682 -0.494906486 -0.496800054 -0.52278517
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.523308863 -0.527913521 -0.535408592 -0.539435104 -0.542252225
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.555961591 -0.569277353 -0.581015956 -0.581916282 -0.603132172
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.612216239 -0.632877207 -0.657107195 -0.665162495 -0.684832772
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.709372748 -0.731309262 -0.794196933 -0.827893652 -0.900691872
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.96572225 0.148517432 0.363798869 0.379063726 0.451182501
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 0.840437155 1.216401792 1.559973376 1.977427802 2.414894519
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 2.647357137 2.799948184 inode3122 inode3123 inode3151 inode3159
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##
##
## Half life (another way of reporting alpha)
## -0.080031991 -0.177729566 -0.288225932 -0.325407223 -0.336320973
## 308643937 308643937 308643937 308643937 308643937
## -0.343935613 -0.347029762 -0.36429282 -0.422992017 -0.425565648
## 308643937 308643937 308643937 308643937 308643937
## -0.428224485 -0.449261397 -0.461474263 -0.463654083 -0.466734078
## 308643937 308643937 308643937 308643937 308643937
## -0.467614451 -0.478411682 -0.494906486 -0.496800054 -0.52278517
## 308643937 308643937 308643937 308643937 308643937
## -0.523308863 -0.527913521 -0.535408592 -0.539435104 -0.542252225
## 308643937 308643937 308643937 308643937 308643937
## -0.555961591 -0.569277353 -0.581015956 -0.581916282 -0.603132172
## 308643937 308643937 308643937 308643937 308643937
## -0.612216239 -0.632877207 -0.657107195 -0.665162495 -0.684832772
## 308643937 308643937 308643937 308643937 308643937
## -0.709372748 -0.731309262 -0.794196933 -0.827893652 -0.900691872
## 308643937 308643937 308643937 308643937 308643937
## -0.96572225 0.148517432 0.363798869 0.379063726 0.451182501
## 308643937 308643937 308643937 308643937 308643937
## 0.840437155 1.216401792 1.559973376 1.977427802 2.414894519
## 308643937 308643937 308643937 308643937 308643937
## 2.647357137 2.799948184 inode3122 inode3123 inode3151
## 308643937 308643937 308643937 308643937 308643937
## inode3159 inode3160 inode3162 inode3217 inode3218
## 308643937 308643937 308643937 308643937 308643937
## inode3219 inode3238 inode3239 inode3241 inode3242
## 308643937 308643937 308643937 308643937 308643937
## inode3246 inode3259 inode3264 inode3269 inode3272
## 308643937 308643937 308643937 308643937 308643937
## inode3274 inode3279 inode3280 inode3282 inode3284
## 308643937 308643937 308643937 308643937 308643937
## inode3288 inode3290 inode3297 inode3301 inode3315
## 308643937 308643937 308643937 308643937 308643937
## inode3316 inode3319 inode3326 inode3351 inode3490
## 308643937 308643937 308643937 308643937 308643937
## inode3495 inode3496 inode3501 inode3502 inode3509
## 308643937 308643937 308643937 308643937 308643937
## inode3513 inode3514 inode3525 inode3538 inode3542
## 308643937 308643937 308643937 308643937 308643937
## inode3572 inode3631 inode3714 inode3732 inode3769
## 308643937 308643937 308643937 308643937 308643937
## inode3970 inode4032 inode4086
## 308643937 308643937 308643937
##
## Arrived at a reliable solution
OU1_ePLA2$eigval
## [1] 2.6e+01 1.3e-06
OU1_ePLA2$solution.se
## -0.080031991 -0.177729566 -0.288225932 -0.325407223 -0.336320973
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.343935613 -0.347029762 -0.36429282 -0.422992017 -0.425565648
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.428224485 -0.449261397 -0.461474263 -0.463654083 -0.466734078
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.467614451 -0.478411682 -0.494906486 -0.496800054 -0.52278517
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.523308863 -0.527913521 -0.535408592 -0.539435104 -0.542252225
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.555961591 -0.569277353 -0.581015956 -0.581916282 -0.603132172
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.612216239 -0.632877207 -0.657107195 -0.665162495 -0.684832772
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.709372748 -0.731309262 -0.794196933 -0.827893652 -0.900691872
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.96572225 0.148517432 0.363798869 0.379063726 0.451182501
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## 0.840437155 1.216401792 1.559973376 1.977427802 2.414894519
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## 2.647357137 2.799948184 inode3122 inode3123 inode3151
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3159 inode3160 inode3162 inode3217 inode3218
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3219 inode3238 inode3239 inode3241 inode3242
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3246 inode3259 inode3264 inode3269 inode3272
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3274 inode3279 inode3280 inode3282 inode3284
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3288 inode3290 inode3297 inode3301 inode3315
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3316 inode3319 inode3326 inode3351 inode3490
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3495 inode3496 inode3501 inode3502 inode3509
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3513 inode3514 inode3525 inode3538 inode3542
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3572 inode3631 inode3714 inode3732 inode3769
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3970 inode4032 inode4086
## alpha 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103
OUM_ePLA2<-OUwie(phy = simmap.tre, data = dat, model="OUM", simmap.tree=T,diagn = T)
## Warning: You might not have enough data to fit this model well
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
OUM_ePLA2
##
## Fit
## lnL AIC AICc BIC model ntax
## 85.24088 -152.4818 -148.196 -134.9206 OUM 52
##
##
## Rates
## 1 2 3 4 5 6
## alpha 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949
## sigma.sq 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326
## 7
## alpha 5.78373949
## sigma.sq 0.02552326
##
## Optima
## 1 2 3 4 5 6
## estimate 0.98278962 1.99999991 3.00016183 3.94380311 4.98768103 6.00000000
## se 0.03331039 0.04697305 0.01001451 0.02575421 0.01410894 0.03321496
## 7
## estimate 6.99998674
## se 0.01485411
##
##
## Half life (another way of reporting alpha)
## 1 2 3 4 5 6 7
## 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441
##
## Arrived at a reliable solution
aic<-setNames(c(BM1_ePLA2$AICc,OU1_ePLA2$AICc,OUM_ePLA2$AICc),
c("BM","OU1","OUM"))
aic
## BM OU1 OUM
## 158.5073 160.7624 -148.1960
aic.w(aic)
## BM OU1 OUM
## 0 0 1
dat<-read.csv("./data/Ouwie_data/CRISP_OUwie_ManyOptions_optima.csv")
BM1_CRISP<-OUwie(phy = simmap.tre,data = dat,model="BM1",simmap.tree=TRUE,diagn = T)
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
BM1_CRISP
##
## Fit
## lnL AIC AICc BIC model ntax
## -137.289 278.578 278.8229 282.4805 BM1 52
##
## Rates
## -0.00423934 -0.175256643 -0.188704348 -0.19150365 -0.230786313
## alpha NA NA NA NA NA
## sigma.sq 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955
## -0.275282586 -0.285641449 -0.30479064 -0.325766959 -0.343935613
## alpha NA NA NA NA NA
## sigma.sq 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955
## -0.347144146 -0.348993029 -0.359161832 -0.361858128 -0.363737891
## alpha NA NA NA NA NA
## sigma.sq 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955
## -0.364251376 -0.371802781 -0.380235729 -0.3861934 -0.399213836
## alpha NA NA NA NA NA
## sigma.sq 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955
## -0.401335606 -0.412305063 -0.415183185 -0.421663658 -0.422514101
## alpha NA NA NA NA NA
## sigma.sq 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955
## -0.422992017 -0.423308801 -0.445491375 -0.448434866 -0.452125326
## alpha NA NA NA NA NA
## sigma.sq 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955
## -0.454790159 -0.466734078 -0.473209269 -0.505966472 -0.512396631
## alpha NA NA NA NA NA
## sigma.sq 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955
## -0.517082249 -0.543732229 -0.552677293 -0.555961591 -0.581015956
## alpha NA NA NA NA NA
## sigma.sq 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955
## -0.585182207 -0.590292055 -0.632877207 -0.655609114 -0.705954615
## alpha NA NA NA NA NA
## sigma.sq 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955
## -0.773362074 -0.900691872 0.046644937 0.077062158 0.079914355
## alpha NA NA NA NA NA
## sigma.sq 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955
## 0.146321473 0.317538642 inode3122 inode3123 inode3151 inode3159
## alpha NA NA NA NA NA NA
## sigma.sq 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955
## inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## alpha NA NA NA NA NA NA
## sigma.sq 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955
## inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## alpha NA NA NA NA NA NA
## sigma.sq 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955
## inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## alpha NA NA NA NA NA NA
## sigma.sq 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955
## inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## alpha NA NA NA NA NA NA
## sigma.sq 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955
## inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## alpha NA NA NA NA NA NA
## sigma.sq 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955
## inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## alpha NA NA NA NA NA NA
## sigma.sq 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955
## inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## alpha NA NA NA NA NA NA
## sigma.sq 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955
## inode3732 inode3769 inode3970 inode4032 inode4086
## alpha NA NA NA NA NA
## sigma.sq 0.4859955 0.4859955 0.4859955 0.4859955 0.4859955
##
## Optima
## -0.00423934 -0.175256643 -0.188704348 -0.19150365 -0.230786313
## estimate -0.8351102 0 0 0 0
## se 2.3090445 0 0 0 0
## -0.275282586 -0.285641449 -0.30479064 -0.325766959 -0.343935613
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.347144146 -0.348993029 -0.359161832 -0.361858128 -0.363737891
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.364251376 -0.371802781 -0.380235729 -0.3861934 -0.399213836
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.401335606 -0.412305063 -0.415183185 -0.421663658 -0.422514101
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.422992017 -0.423308801 -0.445491375 -0.448434866 -0.452125326
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.454790159 -0.466734078 -0.473209269 -0.505966472 -0.512396631
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.517082249 -0.543732229 -0.552677293 -0.555961591 -0.581015956
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.585182207 -0.590292055 -0.632877207 -0.655609114 -0.705954615
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.773362074 -0.900691872 0.046644937 0.077062158 0.079914355
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 0.146321473 0.317538642 inode3122 inode3123 inode3151 inode3159
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 0 0 0 0 0
## se 0 0 0 0 0
##
## Arrived at a reliable solution
OU1_CRISP<-OUwie(phy = simmap.tre, data = dat, model="OU1", simmap.tree=T,diagn = T)
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
OU1_CRISP
##
## Fit
## lnL AIC AICc BIC model ntax
## -133.7486 273.4972 273.9972 279.3509 OU1 52
##
## Rates
## -0.00423934 -0.175256643 -0.188704348 -0.19150365 -0.230786313
## alpha 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785
## sigma.sq 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654
## -0.275282586 -0.285641449 -0.30479064 -0.325766959 -0.343935613
## alpha 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785
## sigma.sq 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654
## -0.347144146 -0.348993029 -0.359161832 -0.361858128 -0.363737891
## alpha 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785
## sigma.sq 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654
## -0.364251376 -0.371802781 -0.380235729 -0.3861934 -0.399213836
## alpha 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785
## sigma.sq 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654
## -0.401335606 -0.412305063 -0.415183185 -0.421663658 -0.422514101
## alpha 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785
## sigma.sq 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654
## -0.422992017 -0.423308801 -0.445491375 -0.448434866 -0.452125326
## alpha 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785
## sigma.sq 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654
## -0.454790159 -0.466734078 -0.473209269 -0.505966472 -0.512396631
## alpha 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785
## sigma.sq 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654
## -0.517082249 -0.543732229 -0.552677293 -0.555961591 -0.581015956
## alpha 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785
## sigma.sq 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654
## -0.585182207 -0.590292055 -0.632877207 -0.655609114 -0.705954615
## alpha 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785
## sigma.sq 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654
## -0.773362074 -0.900691872 0.046644937 0.077062158 0.079914355
## alpha 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785
## sigma.sq 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654
## 0.146321473 0.317538642 inode3122 inode3123 inode3151
## alpha 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785
## sigma.sq 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654
## inode3159 inode3160 inode3162 inode3217 inode3218 inode3219
## alpha 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785
## sigma.sq 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654
## inode3238 inode3239 inode3241 inode3242 inode3246 inode3259
## alpha 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785
## sigma.sq 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654
## inode3264 inode3269 inode3272 inode3274 inode3279 inode3280
## alpha 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785
## sigma.sq 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654
## inode3282 inode3284 inode3288 inode3290 inode3297 inode3301
## alpha 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785
## sigma.sq 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654
## inode3315 inode3316 inode3319 inode3326 inode3351 inode3490
## alpha 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785
## sigma.sq 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654
## inode3495 inode3496 inode3501 inode3502 inode3509 inode3513
## alpha 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785
## sigma.sq 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654
## inode3514 inode3525 inode3538 inode3542 inode3572 inode3631
## alpha 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785
## sigma.sq 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654
## inode3714 inode3732 inode3769 inode3970 inode4032 inode4086
## alpha 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785 0.04184785
## sigma.sq 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654 1.03527654
##
##
## Optima
## -0.00423934 -0.175256643 -0.188704348 -0.19150365 -0.230786313
## estimate -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855
## se 0.7758632 0.7758632 0.7758632 0.7758632 0.7758632
## -0.275282586 -0.285641449 -0.30479064 -0.325766959 -0.343935613
## estimate -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855
## se 0.7758632 0.7758632 0.7758632 0.7758632 0.7758632
## -0.347144146 -0.348993029 -0.359161832 -0.361858128 -0.363737891
## estimate -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855
## se 0.7758632 0.7758632 0.7758632 0.7758632 0.7758632
## -0.364251376 -0.371802781 -0.380235729 -0.3861934 -0.399213836
## estimate -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855
## se 0.7758632 0.7758632 0.7758632 0.7758632 0.7758632
## -0.401335606 -0.412305063 -0.415183185 -0.421663658 -0.422514101
## estimate -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855
## se 0.7758632 0.7758632 0.7758632 0.7758632 0.7758632
## -0.422992017 -0.423308801 -0.445491375 -0.448434866 -0.452125326
## estimate -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855
## se 0.7758632 0.7758632 0.7758632 0.7758632 0.7758632
## -0.454790159 -0.466734078 -0.473209269 -0.505966472 -0.512396631
## estimate -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855
## se 0.7758632 0.7758632 0.7758632 0.7758632 0.7758632
## -0.517082249 -0.543732229 -0.552677293 -0.555961591 -0.581015956
## estimate -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855
## se 0.7758632 0.7758632 0.7758632 0.7758632 0.7758632
## -0.585182207 -0.590292055 -0.632877207 -0.655609114 -0.705954615
## estimate -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855
## se 0.7758632 0.7758632 0.7758632 0.7758632 0.7758632
## -0.773362074 -0.900691872 0.046644937 0.077062158 0.079914355
## estimate -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855
## se 0.7758632 0.7758632 0.7758632 0.7758632 0.7758632
## 0.146321473 0.317538642 inode3122 inode3123 inode3151
## estimate -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855
## se 0.7758632 0.7758632 0.7758632 0.7758632 0.7758632
## inode3159 inode3160 inode3162 inode3217 inode3218 inode3219
## estimate -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855
## se 0.7758632 0.7758632 0.7758632 0.7758632 0.7758632 0.7758632
## inode3238 inode3239 inode3241 inode3242 inode3246 inode3259
## estimate -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855
## se 0.7758632 0.7758632 0.7758632 0.7758632 0.7758632 0.7758632
## inode3264 inode3269 inode3272 inode3274 inode3279 inode3280
## estimate -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855
## se 0.7758632 0.7758632 0.7758632 0.7758632 0.7758632 0.7758632
## inode3282 inode3284 inode3288 inode3290 inode3297 inode3301
## estimate -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855
## se 0.7758632 0.7758632 0.7758632 0.7758632 0.7758632 0.7758632
## inode3315 inode3316 inode3319 inode3326 inode3351 inode3490
## estimate -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855
## se 0.7758632 0.7758632 0.7758632 0.7758632 0.7758632 0.7758632
## inode3495 inode3496 inode3501 inode3502 inode3509 inode3513
## estimate -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855
## se 0.7758632 0.7758632 0.7758632 0.7758632 0.7758632 0.7758632
## inode3514 inode3525 inode3538 inode3542 inode3572 inode3631
## estimate -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855
## se 0.7758632 0.7758632 0.7758632 0.7758632 0.7758632 0.7758632
## inode3714 inode3732 inode3769 inode3970 inode4032 inode4086
## estimate -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855 -0.9053855
## se 0.7758632 0.7758632 0.7758632 0.7758632 0.7758632 0.7758632
##
##
## Half life (another way of reporting alpha)
## -0.00423934 -0.175256643 -0.188704348 -0.19150365 -0.230786313
## 16.56351 16.56351 16.56351 16.56351 16.56351
## -0.275282586 -0.285641449 -0.30479064 -0.325766959 -0.343935613
## 16.56351 16.56351 16.56351 16.56351 16.56351
## -0.347144146 -0.348993029 -0.359161832 -0.361858128 -0.363737891
## 16.56351 16.56351 16.56351 16.56351 16.56351
## -0.364251376 -0.371802781 -0.380235729 -0.3861934 -0.399213836
## 16.56351 16.56351 16.56351 16.56351 16.56351
## -0.401335606 -0.412305063 -0.415183185 -0.421663658 -0.422514101
## 16.56351 16.56351 16.56351 16.56351 16.56351
## -0.422992017 -0.423308801 -0.445491375 -0.448434866 -0.452125326
## 16.56351 16.56351 16.56351 16.56351 16.56351
## -0.454790159 -0.466734078 -0.473209269 -0.505966472 -0.512396631
## 16.56351 16.56351 16.56351 16.56351 16.56351
## -0.517082249 -0.543732229 -0.552677293 -0.555961591 -0.581015956
## 16.56351 16.56351 16.56351 16.56351 16.56351
## -0.585182207 -0.590292055 -0.632877207 -0.655609114 -0.705954615
## 16.56351 16.56351 16.56351 16.56351 16.56351
## -0.773362074 -0.900691872 0.046644937 0.077062158 0.079914355
## 16.56351 16.56351 16.56351 16.56351 16.56351
## 0.146321473 0.317538642 inode3122 inode3123 inode3151
## 16.56351 16.56351 16.56351 16.56351 16.56351
## inode3159 inode3160 inode3162 inode3217 inode3218
## 16.56351 16.56351 16.56351 16.56351 16.56351
## inode3219 inode3238 inode3239 inode3241 inode3242
## 16.56351 16.56351 16.56351 16.56351 16.56351
## inode3246 inode3259 inode3264 inode3269 inode3272
## 16.56351 16.56351 16.56351 16.56351 16.56351
## inode3274 inode3279 inode3280 inode3282 inode3284
## 16.56351 16.56351 16.56351 16.56351 16.56351
## inode3288 inode3290 inode3297 inode3301 inode3315
## 16.56351 16.56351 16.56351 16.56351 16.56351
## inode3316 inode3319 inode3326 inode3351 inode3490
## 16.56351 16.56351 16.56351 16.56351 16.56351
## inode3495 inode3496 inode3501 inode3502 inode3509
## 16.56351 16.56351 16.56351 16.56351 16.56351
## inode3513 inode3514 inode3525 inode3538 inode3542
## 16.56351 16.56351 16.56351 16.56351 16.56351
## inode3572 inode3631 inode3714 inode3732 inode3769
## 16.56351 16.56351 16.56351 16.56351 16.56351
## inode3970 inode4032 inode4086
## 16.56351 16.56351 16.56351
##
## Arrived at a reliable solution
OU1_CRISP$eigval
## [1] 40.0 2.2
OU1_CRISP$solution.se
## -0.00423934 -0.175256643 -0.188704348 -0.19150365 -0.230786313
## alpha 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137
## sigma.sq 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450
## -0.275282586 -0.285641449 -0.30479064 -0.325766959 -0.343935613
## alpha 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137
## sigma.sq 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450
## -0.347144146 -0.348993029 -0.359161832 -0.361858128 -0.363737891
## alpha 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137
## sigma.sq 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450
## -0.364251376 -0.371802781 -0.380235729 -0.3861934 -0.399213836
## alpha 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137
## sigma.sq 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450
## -0.401335606 -0.412305063 -0.415183185 -0.421663658 -0.422514101
## alpha 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137
## sigma.sq 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450
## -0.422992017 -0.423308801 -0.445491375 -0.448434866 -0.452125326
## alpha 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137
## sigma.sq 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450
## -0.454790159 -0.466734078 -0.473209269 -0.505966472 -0.512396631
## alpha 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137
## sigma.sq 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450
## -0.517082249 -0.543732229 -0.552677293 -0.555961591 -0.581015956
## alpha 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137
## sigma.sq 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450
## -0.585182207 -0.590292055 -0.632877207 -0.655609114 -0.705954615
## alpha 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137
## sigma.sq 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450
## -0.773362074 -0.900691872 0.046644937 0.077062158 0.079914355
## alpha 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137
## sigma.sq 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450
## 0.146321473 0.317538642 inode3122 inode3123 inode3151 inode3159
## alpha 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137
## sigma.sq 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450
## inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## alpha 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137
## sigma.sq 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450
## inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## alpha 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137
## sigma.sq 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450
## inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## alpha 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137
## sigma.sq 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450
## inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## alpha 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137
## sigma.sq 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450
## inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## alpha 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137
## sigma.sq 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450
## inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## alpha 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137
## sigma.sq 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450
## inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## alpha 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137
## sigma.sq 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450
## inode3732 inode3769 inode3970 inode4032 inode4086
## alpha 0.5508137 0.5508137 0.5508137 0.5508137 0.5508137
## sigma.sq 0.4314450 0.4314450 0.4314450 0.4314450 0.4314450
OUM_CRISP<-OUwie(phy = simmap.tre, data = dat, model="OUM", simmap.tree=T,diagn = T)
## Warning: You might not have enough data to fit this model well
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
OUM_CRISP
##
## Fit
## lnL AIC AICc BIC model ntax
## -130.0814 278.1628 282.4485 295.724 OUM 52
##
##
## Rates
## 1 2 3 4 5 6
## alpha 0.07936546 0.07936546 0.07936546 0.07936546 0.07936546 0.07936546
## sigma.sq 1.49397240 1.49397240 1.49397240 1.49397240 1.49397240 1.49397240
## 7
## alpha 0.07936546
## sigma.sq 1.49397240
##
## Optima
## 1 2 3 4 5 6
## estimate 17.60332 -3.376277 -0.4272226 -18.87897 -1.082753 -12.66602
## se 14.70393 15.399011 0.8541136 15.23660 1.272570 4.25283
## 7
## estimate -1.4030843
## se 0.9571823
##
##
## Half life (another way of reporting alpha)
## 1 2 3 4 5 6 7
## 8.733613 8.733613 8.733613 8.733613 8.733613 8.733613 8.733613
##
## Arrived at a reliable solution
aic<-setNames(c(BM1_CRISP$AICc,OU1_CRISP$AICc,OUM_CRISP$AICc),
c("BM","OU1","OUM"))
aic
## BM OU1 OUM
## 278.8229 273.9972 282.4485
aic.w(aic)
## BM OU1 OUM
## 0.08110998 0.90565318 0.01323684
dat<-read.csv("./data/Ouwie_data/CTL_OUwie_ManyOptions_optima.csv")
BM1_CTL<-OUwie(phy = simmap.tre,data = dat,model="BM1",simmap.tree=TRUE,diagn = T)
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
BM1_CTL
##
## Fit
## lnL AIC AICc BIC model ntax
## -77.13118 158.2624 158.5073 162.1649 BM1 52
##
## Rates
## -0.022042567 -0.048848102 -0.069369685 -0.143116735 -0.155979758
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.165286797 -0.174476052 -0.188704348 -0.195619323 -0.220512224
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.226062663 -0.228813899 -0.24113775 -0.277340249 -0.294827343
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.308103582 -0.311026741 -0.334277933 -0.343935613 -0.356004113
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.358105881 -0.360796274 -0.368734945 -0.391676306 -0.399213836
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.399284019 -0.422514101 -0.434039154 -0.434819003 -0.454790159
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.477252011 -0.488514042 -0.495372826 -0.512363785 -0.525462681
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.528882243 -0.563339519 -0.585182207 -0.61894364 -0.770282542
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 0.042311594 0.051575301 0.053864522 0.388086563 0.399697418
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 0.404400547 0.476569918 0.539741198 0.822821283 0.845268561
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 1.092955666 1.698437739 inode3122 inode3123 inode3151
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3159 inode3160 inode3162 inode3217 inode3218 inode3219
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3238 inode3239 inode3241 inode3242 inode3246 inode3259
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3264 inode3269 inode3272 inode3274 inode3279 inode3280
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3282 inode3284 inode3288 inode3290 inode3297 inode3301
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3315 inode3316 inode3319 inode3326 inode3351 inode3490
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3495 inode3496 inode3501 inode3502 inode3509 inode3513
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3514 inode3525 inode3538 inode3542 inode3572 inode3631
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3714 inode3732 inode3769 inode3970 inode4032 inode4086
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##
## Optima
## -0.022042567 -0.048848102 -0.069369685 -0.143116735 -0.155979758
## estimate 4.0576335 0 0 0 0
## se 0.7261147 0 0 0 0
## -0.165286797 -0.174476052 -0.188704348 -0.195619323 -0.220512224
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.226062663 -0.228813899 -0.24113775 -0.277340249 -0.294827343
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.308103582 -0.311026741 -0.334277933 -0.343935613 -0.356004113
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.358105881 -0.360796274 -0.368734945 -0.391676306 -0.399213836
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.399284019 -0.422514101 -0.434039154 -0.434819003 -0.454790159
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.477252011 -0.488514042 -0.495372826 -0.512363785 -0.525462681
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.528882243 -0.563339519 -0.585182207 -0.61894364 -0.770282542
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 0.042311594 0.051575301 0.053864522 0.388086563 0.399697418
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 0.404400547 0.476569918 0.539741198 0.822821283 0.845268561
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 1.092955666 1.698437739 inode3122 inode3123 inode3151 inode3159
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 0 0 0 0 0
## se 0 0 0 0 0
##
## Arrived at a reliable solution
OU1_CTL<-OUwie(phy = simmap.tre, data = dat, model="OU1", simmap.tree=T,diagn = T)
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
OU1_CTL
##
## Fit
## lnL AIC AICc BIC model ntax
## -77.13118 160.2624 160.7624 166.1161 OU1 52
##
## Rates
## -0.022042567 -0.048848102 -0.069369685 -0.143116735 -0.155979758
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.165286797 -0.174476052 -0.188704348 -0.195619323 -0.220512224
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.226062663 -0.228813899 -0.24113775 -0.277340249 -0.294827343
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.308103582 -0.311026741 -0.334277933 -0.343935613 -0.356004113
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.358105881 -0.360796274 -0.368734945 -0.391676306 -0.399213836
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.399284019 -0.422514101 -0.434039154 -0.434819003 -0.454790159
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.477252011 -0.488514042 -0.495372826 -0.512363785 -0.525462681
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.528882243 -0.563339519 -0.585182207 -0.61894364 -0.770282542
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## 0.042311594 0.051575301 0.053864522 0.388086563 0.399697418
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## 0.404400547 0.476569918 0.539741198 0.822821283 0.845268561
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## 1.092955666 1.698437739 inode3122 inode3123 inode3151
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3159 inode3160 inode3162 inode3217 inode3218
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3219 inode3238 inode3239 inode3241 inode3242
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3246 inode3259 inode3264 inode3269 inode3272
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3274 inode3279 inode3280 inode3282 inode3284
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3288 inode3290 inode3297 inode3301 inode3315
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3316 inode3319 inode3326 inode3351 inode3490
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3495 inode3496 inode3501 inode3502 inode3509
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3513 inode3514 inode3525 inode3538 inode3542
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3572 inode3631 inode3714 inode3732 inode3769
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3970 inode4032 inode4086
## alpha 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02
##
##
## Optima
## -0.022042567 -0.048848102 -0.069369685 -0.143116735 -0.155979758
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.165286797 -0.174476052 -0.188704348 -0.195619323 -0.220512224
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.226062663 -0.228813899 -0.24113775 -0.277340249 -0.294827343
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.308103582 -0.311026741 -0.334277933 -0.343935613 -0.356004113
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.358105881 -0.360796274 -0.368734945 -0.391676306 -0.399213836
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.399284019 -0.422514101 -0.434039154 -0.434819003 -0.454790159
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.477252011 -0.488514042 -0.495372826 -0.512363785 -0.525462681
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.528882243 -0.563339519 -0.585182207 -0.61894364 -0.770282542
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 0.042311594 0.051575301 0.053864522 0.388086563 0.399697418
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 0.404400547 0.476569918 0.539741198 0.822821283 0.845268561
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 1.092955666 1.698437739 inode3122 inode3123 inode3151 inode3159
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##
##
## Half life (another way of reporting alpha)
## -0.022042567 -0.048848102 -0.069369685 -0.143116735 -0.155979758
## 308643937 308643937 308643937 308643937 308643937
## -0.165286797 -0.174476052 -0.188704348 -0.195619323 -0.220512224
## 308643937 308643937 308643937 308643937 308643937
## -0.226062663 -0.228813899 -0.24113775 -0.277340249 -0.294827343
## 308643937 308643937 308643937 308643937 308643937
## -0.308103582 -0.311026741 -0.334277933 -0.343935613 -0.356004113
## 308643937 308643937 308643937 308643937 308643937
## -0.358105881 -0.360796274 -0.368734945 -0.391676306 -0.399213836
## 308643937 308643937 308643937 308643937 308643937
## -0.399284019 -0.422514101 -0.434039154 -0.434819003 -0.454790159
## 308643937 308643937 308643937 308643937 308643937
## -0.477252011 -0.488514042 -0.495372826 -0.512363785 -0.525462681
## 308643937 308643937 308643937 308643937 308643937
## -0.528882243 -0.563339519 -0.585182207 -0.61894364 -0.770282542
## 308643937 308643937 308643937 308643937 308643937
## 0.042311594 0.051575301 0.053864522 0.388086563 0.399697418
## 308643937 308643937 308643937 308643937 308643937
## 0.404400547 0.476569918 0.539741198 0.822821283 0.845268561
## 308643937 308643937 308643937 308643937 308643937
## 1.092955666 1.698437739 inode3122 inode3123 inode3151
## 308643937 308643937 308643937 308643937 308643937
## inode3159 inode3160 inode3162 inode3217 inode3218
## 308643937 308643937 308643937 308643937 308643937
## inode3219 inode3238 inode3239 inode3241 inode3242
## 308643937 308643937 308643937 308643937 308643937
## inode3246 inode3259 inode3264 inode3269 inode3272
## 308643937 308643937 308643937 308643937 308643937
## inode3274 inode3279 inode3280 inode3282 inode3284
## 308643937 308643937 308643937 308643937 308643937
## inode3288 inode3290 inode3297 inode3301 inode3315
## 308643937 308643937 308643937 308643937 308643937
## inode3316 inode3319 inode3326 inode3351 inode3490
## 308643937 308643937 308643937 308643937 308643937
## inode3495 inode3496 inode3501 inode3502 inode3509
## 308643937 308643937 308643937 308643937 308643937
## inode3513 inode3514 inode3525 inode3538 inode3542
## 308643937 308643937 308643937 308643937 308643937
## inode3572 inode3631 inode3714 inode3732 inode3769
## 308643937 308643937 308643937 308643937 308643937
## inode3970 inode4032 inode4086
## 308643937 308643937 308643937
##
## Arrived at a reliable solution
OU1_CTL$eigval
## [1] 2.6e+01 1.3e-06
OU1_CTL$solution.se
## -0.022042567 -0.048848102 -0.069369685 -0.143116735 -0.155979758
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.165286797 -0.174476052 -0.188704348 -0.195619323 -0.220512224
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.226062663 -0.228813899 -0.24113775 -0.277340249 -0.294827343
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.308103582 -0.311026741 -0.334277933 -0.343935613 -0.356004113
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.358105881 -0.360796274 -0.368734945 -0.391676306 -0.399213836
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.399284019 -0.422514101 -0.434039154 -0.434819003 -0.454790159
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.477252011 -0.488514042 -0.495372826 -0.512363785 -0.525462681
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.528882243 -0.563339519 -0.585182207 -0.61894364 -0.770282542
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## 0.042311594 0.051575301 0.053864522 0.388086563 0.399697418
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## 0.404400547 0.476569918 0.539741198 0.822821283 0.845268561
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## 1.092955666 1.698437739 inode3122 inode3123 inode3151
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3159 inode3160 inode3162 inode3217 inode3218
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3219 inode3238 inode3239 inode3241 inode3242
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3246 inode3259 inode3264 inode3269 inode3272
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3274 inode3279 inode3280 inode3282 inode3284
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3288 inode3290 inode3297 inode3301 inode3315
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3316 inode3319 inode3326 inode3351 inode3490
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3495 inode3496 inode3501 inode3502 inode3509
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3513 inode3514 inode3525 inode3538 inode3542
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3572 inode3631 inode3714 inode3732 inode3769
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3970 inode4032 inode4086
## alpha 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103
OUM_CTL<-OUwie(phy = simmap.tre, data = dat, model="OUM", simmap.tree=T,diagn = T)
## Warning: You might not have enough data to fit this model well
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
OUM_CTL
##
## Fit
## lnL AIC AICc BIC model ntax
## 85.24088 -152.4818 -148.196 -134.9206 OUM 52
##
##
## Rates
## 1 2 3 4 5 6
## alpha 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949
## sigma.sq 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326
## 7
## alpha 5.78373949
## sigma.sq 0.02552326
##
## Optima
## 1 2 3 4 5 6
## estimate 0.98278962 1.99999991 3.00016183 3.94380311 4.98768103 6.00000000
## se 0.03331039 0.04697305 0.01001451 0.02575421 0.01410894 0.03321496
## 7
## estimate 6.99998674
## se 0.01485411
##
##
## Half life (another way of reporting alpha)
## 1 2 3 4 5 6 7
## 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441
##
## Arrived at a reliable solution
aic<-setNames(c(BM1_CTL$AICc,OU1_CTL$AICc,OUM_CTL$AICc),
c("BM","OU1","OUM"))
aic
## BM OU1 OUM
## 158.5073 160.7624 -148.1960
aic.w(aic)
## BM OU1 OUM
## 0 0 1
dat<-read.csv("./data/Ouwie_data/GF_OUwie_ManyOptions_optima.csv")
BM1_GF<-OUwie(phy = simmap.tre,data = dat,model="BM1",simmap.tree=TRUE,diagn = T)
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
BM1_GF
##
## Fit
## lnL AIC AICc BIC model ntax
## -77.13118 158.2624 158.5073 162.1649 BM1 52
##
## Rates
## -0.101480746 -0.199120618 -0.208294348 -0.223619452 -0.282532123
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.282712808 -0.310359147 -0.310940604 -0.324668291 -0.325799169
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.339426699 -0.347029762 -0.359161832 -0.368572056 -0.384774302
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.389184624 -0.396332642 -0.399213836 -0.399284019 -0.404661486
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.409662437 -0.419808798 -0.423308801 -0.425565648 -0.42583897
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.438880858 -0.448896787 -0.454790159 -0.45813357 -0.460589809
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.462169254 -0.462264075 -0.463092209 -0.473210272 -0.481264314
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.491651278 -0.535408592 -0.539435104 -0.546444401 -0.555961591
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.562419106 -0.575631106 -0.601151125 -0.603132172 -0.609558762
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.612242656 -0.651847915 -0.654661809 -0.681722879 -0.900691872
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 0.079914355 1.349473949 inode3122 inode3123 inode3151
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3159 inode3160 inode3162 inode3217 inode3218 inode3219
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3238 inode3239 inode3241 inode3242 inode3246 inode3259
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3264 inode3269 inode3272 inode3274 inode3279 inode3280
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3282 inode3284 inode3288 inode3290 inode3297 inode3301
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3315 inode3316 inode3319 inode3326 inode3351 inode3490
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3495 inode3496 inode3501 inode3502 inode3509 inode3513
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3514 inode3525 inode3538 inode3542 inode3572 inode3631
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3714 inode3732 inode3769 inode3970 inode4032 inode4086
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##
## Optima
## -0.101480746 -0.199120618 -0.208294348 -0.223619452 -0.282532123
## estimate 4.0576335 0 0 0 0
## se 0.7261147 0 0 0 0
## -0.282712808 -0.310359147 -0.310940604 -0.324668291 -0.325799169
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.339426699 -0.347029762 -0.359161832 -0.368572056 -0.384774302
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.389184624 -0.396332642 -0.399213836 -0.399284019 -0.404661486
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.409662437 -0.419808798 -0.423308801 -0.425565648 -0.42583897
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.438880858 -0.448896787 -0.454790159 -0.45813357 -0.460589809
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.462169254 -0.462264075 -0.463092209 -0.473210272 -0.481264314
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.491651278 -0.535408592 -0.539435104 -0.546444401 -0.555961591
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.562419106 -0.575631106 -0.601151125 -0.603132172 -0.609558762
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.612242656 -0.651847915 -0.654661809 -0.681722879 -0.900691872
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 0.079914355 1.349473949 inode3122 inode3123 inode3151 inode3159
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 0 0 0 0 0
## se 0 0 0 0 0
##
## Arrived at a reliable solution
OU1_GF<-OUwie(phy = simmap.tre, data = dat, model="OU1", simmap.tree=T,diagn = T)
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
OU1_GF
##
## Fit
## lnL AIC AICc BIC model ntax
## -77.13118 160.2624 160.7624 166.1161 OU1 52
##
## Rates
## -0.101480746 -0.199120618 -0.208294348 -0.223619452 -0.282532123
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.282712808 -0.310359147 -0.310940604 -0.324668291 -0.325799169
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.339426699 -0.347029762 -0.359161832 -0.368572056 -0.384774302
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.389184624 -0.396332642 -0.399213836 -0.399284019 -0.404661486
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.409662437 -0.419808798 -0.423308801 -0.425565648 -0.42583897
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.438880858 -0.448896787 -0.454790159 -0.45813357 -0.460589809
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.462169254 -0.462264075 -0.463092209 -0.473210272 -0.481264314
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.491651278 -0.535408592 -0.539435104 -0.546444401 -0.555961591
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.562419106 -0.575631106 -0.601151125 -0.603132172 -0.609558762
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.612242656 -0.651847915 -0.654661809 -0.681722879 -0.900691872
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## 0.079914355 1.349473949 inode3122 inode3123 inode3151
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3159 inode3160 inode3162 inode3217 inode3218
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3219 inode3238 inode3239 inode3241 inode3242
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3246 inode3259 inode3264 inode3269 inode3272
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3274 inode3279 inode3280 inode3282 inode3284
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3288 inode3290 inode3297 inode3301 inode3315
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3316 inode3319 inode3326 inode3351 inode3490
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3495 inode3496 inode3501 inode3502 inode3509
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3513 inode3514 inode3525 inode3538 inode3542
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3572 inode3631 inode3714 inode3732 inode3769
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3970 inode4032 inode4086
## alpha 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02
##
##
## Optima
## -0.101480746 -0.199120618 -0.208294348 -0.223619452 -0.282532123
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.282712808 -0.310359147 -0.310940604 -0.324668291 -0.325799169
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.339426699 -0.347029762 -0.359161832 -0.368572056 -0.384774302
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.389184624 -0.396332642 -0.399213836 -0.399284019 -0.404661486
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.409662437 -0.419808798 -0.423308801 -0.425565648 -0.42583897
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.438880858 -0.448896787 -0.454790159 -0.45813357 -0.460589809
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.462169254 -0.462264075 -0.463092209 -0.473210272 -0.481264314
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.491651278 -0.535408592 -0.539435104 -0.546444401 -0.555961591
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.562419106 -0.575631106 -0.601151125 -0.603132172 -0.609558762
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.612242656 -0.651847915 -0.654661809 -0.681722879 -0.900691872
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 0.079914355 1.349473949 inode3122 inode3123 inode3151 inode3159
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##
##
## Half life (another way of reporting alpha)
## -0.101480746 -0.199120618 -0.208294348 -0.223619452 -0.282532123
## 308643937 308643937 308643937 308643937 308643937
## -0.282712808 -0.310359147 -0.310940604 -0.324668291 -0.325799169
## 308643937 308643937 308643937 308643937 308643937
## -0.339426699 -0.347029762 -0.359161832 -0.368572056 -0.384774302
## 308643937 308643937 308643937 308643937 308643937
## -0.389184624 -0.396332642 -0.399213836 -0.399284019 -0.404661486
## 308643937 308643937 308643937 308643937 308643937
## -0.409662437 -0.419808798 -0.423308801 -0.425565648 -0.42583897
## 308643937 308643937 308643937 308643937 308643937
## -0.438880858 -0.448896787 -0.454790159 -0.45813357 -0.460589809
## 308643937 308643937 308643937 308643937 308643937
## -0.462169254 -0.462264075 -0.463092209 -0.473210272 -0.481264314
## 308643937 308643937 308643937 308643937 308643937
## -0.491651278 -0.535408592 -0.539435104 -0.546444401 -0.555961591
## 308643937 308643937 308643937 308643937 308643937
## -0.562419106 -0.575631106 -0.601151125 -0.603132172 -0.609558762
## 308643937 308643937 308643937 308643937 308643937
## -0.612242656 -0.651847915 -0.654661809 -0.681722879 -0.900691872
## 308643937 308643937 308643937 308643937 308643937
## 0.079914355 1.349473949 inode3122 inode3123 inode3151
## 308643937 308643937 308643937 308643937 308643937
## inode3159 inode3160 inode3162 inode3217 inode3218
## 308643937 308643937 308643937 308643937 308643937
## inode3219 inode3238 inode3239 inode3241 inode3242
## 308643937 308643937 308643937 308643937 308643937
## inode3246 inode3259 inode3264 inode3269 inode3272
## 308643937 308643937 308643937 308643937 308643937
## inode3274 inode3279 inode3280 inode3282 inode3284
## 308643937 308643937 308643937 308643937 308643937
## inode3288 inode3290 inode3297 inode3301 inode3315
## 308643937 308643937 308643937 308643937 308643937
## inode3316 inode3319 inode3326 inode3351 inode3490
## 308643937 308643937 308643937 308643937 308643937
## inode3495 inode3496 inode3501 inode3502 inode3509
## 308643937 308643937 308643937 308643937 308643937
## inode3513 inode3514 inode3525 inode3538 inode3542
## 308643937 308643937 308643937 308643937 308643937
## inode3572 inode3631 inode3714 inode3732 inode3769
## 308643937 308643937 308643937 308643937 308643937
## inode3970 inode4032 inode4086
## 308643937 308643937 308643937
##
## Arrived at a reliable solution
OU1_GF$eigval
## [1] 2.6e+01 1.3e-06
OU1_GF$solution.se
## -0.101480746 -0.199120618 -0.208294348 -0.223619452 -0.282532123
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.282712808 -0.310359147 -0.310940604 -0.324668291 -0.325799169
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.339426699 -0.347029762 -0.359161832 -0.368572056 -0.384774302
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.389184624 -0.396332642 -0.399213836 -0.399284019 -0.404661486
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.409662437 -0.419808798 -0.423308801 -0.425565648 -0.42583897
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.438880858 -0.448896787 -0.454790159 -0.45813357 -0.460589809
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.462169254 -0.462264075 -0.463092209 -0.473210272 -0.481264314
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.491651278 -0.535408592 -0.539435104 -0.546444401 -0.555961591
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.562419106 -0.575631106 -0.601151125 -0.603132172 -0.609558762
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.612242656 -0.651847915 -0.654661809 -0.681722879 -0.900691872
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## 0.079914355 1.349473949 inode3122 inode3123 inode3151
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3159 inode3160 inode3162 inode3217 inode3218
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3219 inode3238 inode3239 inode3241 inode3242
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3246 inode3259 inode3264 inode3269 inode3272
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3274 inode3279 inode3280 inode3282 inode3284
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3288 inode3290 inode3297 inode3301 inode3315
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3316 inode3319 inode3326 inode3351 inode3490
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3495 inode3496 inode3501 inode3502 inode3509
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3513 inode3514 inode3525 inode3538 inode3542
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3572 inode3631 inode3714 inode3732 inode3769
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3970 inode4032 inode4086
## alpha 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103
OUM_GF<-OUwie(phy = simmap.tre, data = dat, model="OUM", simmap.tree=T,diagn = T)
## Warning: You might not have enough data to fit this model well
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
OUM_GF
##
## Fit
## lnL AIC AICc BIC model ntax
## 85.24088 -152.4818 -148.196 -134.9206 OUM 52
##
##
## Rates
## 1 2 3 4 5 6
## alpha 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949
## sigma.sq 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326
## 7
## alpha 5.78373949
## sigma.sq 0.02552326
##
## Optima
## 1 2 3 4 5 6
## estimate 0.98278962 1.99999991 3.00016183 3.94380311 4.98768103 6.00000000
## se 0.03331039 0.04697305 0.01001451 0.02575421 0.01410894 0.03321496
## 7
## estimate 6.99998674
## se 0.01485411
##
##
## Half life (another way of reporting alpha)
## 1 2 3 4 5 6 7
## 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441
##
## Arrived at a reliable solution
aic<-setNames(c(BM1_GF$AICc,OU1_GF$AICc,OUM_GF$AICc),
c("BM","OU1","OUM"))
aic
## BM OU1 OUM
## 158.5073 160.7624 -148.1960
aic.w(aic)
## BM OU1 OUM
## 0 0 1
dat<-read.csv("./data/Ouwie_data/BPP_OUwie_ManyOptions_optima.csv")
BM1_BPP<-OUwie(phy = simmap.tre,data = dat,model="BM1",simmap.tree=TRUE,diagn = T)
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
BM1_BPP
##
## Fit
## lnL AIC AICc BIC model ntax
## -77.13118 158.2624 158.5073 162.1649 BM1 52
##
## Rates
## -0.105145425 -0.119084599 -0.188704348 -0.225036539 -0.255317351
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.30627187 -0.327981232 -0.334277933 -0.343935613 -0.347029762
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.359161832 -0.359945235 -0.368913567 -0.380235729 -0.398461713
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.399213836 -0.399284019 -0.408989879 -0.428224485 -0.442200811
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.447400078 -0.449261397 -0.454790159 -0.466734078 -0.467614451
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.471618177 -0.473209269 -0.483120435 -0.494906486 -0.496293077
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.563339519 -0.579918045 -0.581015956 -0.60291507 -0.612242656
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.61894364 -0.652729444 -0.731309262 0.117400503 0.12862613
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 0.447183364 0.510616761 0.519681634 0.627037582 0.788405152
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 1.035253997 1.041012607 1.118621879 1.397025289 1.453249541
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 1.463514021 2.829425593 inode3122 inode3123 inode3151
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3159 inode3160 inode3162 inode3217 inode3218 inode3219
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3238 inode3239 inode3241 inode3242 inode3246 inode3259
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3264 inode3269 inode3272 inode3274 inode3279 inode3280
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3282 inode3284 inode3288 inode3290 inode3297 inode3301
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3315 inode3316 inode3319 inode3326 inode3351 inode3490
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3495 inode3496 inode3501 inode3502 inode3509 inode3513
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3514 inode3525 inode3538 inode3542 inode3572 inode3631
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3714 inode3732 inode3769 inode3970 inode4032 inode4086
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##
## Optima
## -0.105145425 -0.119084599 -0.188704348 -0.225036539 -0.255317351
## estimate 4.0576335 0 0 0 0
## se 0.7261147 0 0 0 0
## -0.30627187 -0.327981232 -0.334277933 -0.343935613 -0.347029762
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.359161832 -0.359945235 -0.368913567 -0.380235729 -0.398461713
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.399213836 -0.399284019 -0.408989879 -0.428224485 -0.442200811
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.447400078 -0.449261397 -0.454790159 -0.466734078 -0.467614451
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.471618177 -0.473209269 -0.483120435 -0.494906486 -0.496293077
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.563339519 -0.579918045 -0.581015956 -0.60291507 -0.612242656
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.61894364 -0.652729444 -0.731309262 0.117400503 0.12862613
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 0.447183364 0.510616761 0.519681634 0.627037582 0.788405152
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 1.035253997 1.041012607 1.118621879 1.397025289 1.453249541
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 1.463514021 2.829425593 inode3122 inode3123 inode3151 inode3159
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 0 0 0 0 0
## se 0 0 0 0 0
##
## Arrived at a reliable solution
OU1_BPP<-OUwie(phy = simmap.tre, data = dat, model="OU1", simmap.tree=T,diagn = T)
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
OU1_BPP
##
## Fit
## lnL AIC AICc BIC model ntax
## -77.13118 160.2624 160.7624 166.1161 OU1 52
##
## Rates
## -0.105145425 -0.119084599 -0.188704348 -0.225036539 -0.255317351
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.30627187 -0.327981232 -0.334277933 -0.343935613 -0.347029762
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.359161832 -0.359945235 -0.368913567 -0.380235729 -0.398461713
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.399213836 -0.399284019 -0.408989879 -0.428224485 -0.442200811
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.447400078 -0.449261397 -0.454790159 -0.466734078 -0.467614451
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.471618177 -0.473209269 -0.483120435 -0.494906486 -0.496293077
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.563339519 -0.579918045 -0.581015956 -0.60291507 -0.612242656
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.61894364 -0.652729444 -0.731309262 0.117400503 0.12862613
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## 0.447183364 0.510616761 0.519681634 0.627037582 0.788405152
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## 1.035253997 1.041012607 1.118621879 1.397025289 1.453249541
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## 1.463514021 2.829425593 inode3122 inode3123 inode3151
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3159 inode3160 inode3162 inode3217 inode3218
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3219 inode3238 inode3239 inode3241 inode3242
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3246 inode3259 inode3264 inode3269 inode3272
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3274 inode3279 inode3280 inode3282 inode3284
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3288 inode3290 inode3297 inode3301 inode3315
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3316 inode3319 inode3326 inode3351 inode3490
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3495 inode3496 inode3501 inode3502 inode3509
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3513 inode3514 inode3525 inode3538 inode3542
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3572 inode3631 inode3714 inode3732 inode3769
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3970 inode4032 inode4086
## alpha 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02
##
##
## Optima
## -0.105145425 -0.119084599 -0.188704348 -0.225036539 -0.255317351
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.30627187 -0.327981232 -0.334277933 -0.343935613 -0.347029762
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.359161832 -0.359945235 -0.368913567 -0.380235729 -0.398461713
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.399213836 -0.399284019 -0.408989879 -0.428224485 -0.442200811
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.447400078 -0.449261397 -0.454790159 -0.466734078 -0.467614451
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.471618177 -0.473209269 -0.483120435 -0.494906486 -0.496293077
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.563339519 -0.579918045 -0.581015956 -0.60291507 -0.612242656
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.61894364 -0.652729444 -0.731309262 0.117400503 0.12862613
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 0.447183364 0.510616761 0.519681634 0.627037582 0.788405152
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 1.035253997 1.041012607 1.118621879 1.397025289 1.453249541
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 1.463514021 2.829425593 inode3122 inode3123 inode3151 inode3159
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##
##
## Half life (another way of reporting alpha)
## -0.105145425 -0.119084599 -0.188704348 -0.225036539 -0.255317351
## 308643937 308643937 308643937 308643937 308643937
## -0.30627187 -0.327981232 -0.334277933 -0.343935613 -0.347029762
## 308643937 308643937 308643937 308643937 308643937
## -0.359161832 -0.359945235 -0.368913567 -0.380235729 -0.398461713
## 308643937 308643937 308643937 308643937 308643937
## -0.399213836 -0.399284019 -0.408989879 -0.428224485 -0.442200811
## 308643937 308643937 308643937 308643937 308643937
## -0.447400078 -0.449261397 -0.454790159 -0.466734078 -0.467614451
## 308643937 308643937 308643937 308643937 308643937
## -0.471618177 -0.473209269 -0.483120435 -0.494906486 -0.496293077
## 308643937 308643937 308643937 308643937 308643937
## -0.563339519 -0.579918045 -0.581015956 -0.60291507 -0.612242656
## 308643937 308643937 308643937 308643937 308643937
## -0.61894364 -0.652729444 -0.731309262 0.117400503 0.12862613
## 308643937 308643937 308643937 308643937 308643937
## 0.447183364 0.510616761 0.519681634 0.627037582 0.788405152
## 308643937 308643937 308643937 308643937 308643937
## 1.035253997 1.041012607 1.118621879 1.397025289 1.453249541
## 308643937 308643937 308643937 308643937 308643937
## 1.463514021 2.829425593 inode3122 inode3123 inode3151
## 308643937 308643937 308643937 308643937 308643937
## inode3159 inode3160 inode3162 inode3217 inode3218
## 308643937 308643937 308643937 308643937 308643937
## inode3219 inode3238 inode3239 inode3241 inode3242
## 308643937 308643937 308643937 308643937 308643937
## inode3246 inode3259 inode3264 inode3269 inode3272
## 308643937 308643937 308643937 308643937 308643937
## inode3274 inode3279 inode3280 inode3282 inode3284
## 308643937 308643937 308643937 308643937 308643937
## inode3288 inode3290 inode3297 inode3301 inode3315
## 308643937 308643937 308643937 308643937 308643937
## inode3316 inode3319 inode3326 inode3351 inode3490
## 308643937 308643937 308643937 308643937 308643937
## inode3495 inode3496 inode3501 inode3502 inode3509
## 308643937 308643937 308643937 308643937 308643937
## inode3513 inode3514 inode3525 inode3538 inode3542
## 308643937 308643937 308643937 308643937 308643937
## inode3572 inode3631 inode3714 inode3732 inode3769
## 308643937 308643937 308643937 308643937 308643937
## inode3970 inode4032 inode4086
## 308643937 308643937 308643937
##
## Arrived at a reliable solution
OU1_BPP$eigval
## [1] 2.6e+01 1.3e-06
OU1_BPP$solution.se
## -0.105145425 -0.119084599 -0.188704348 -0.225036539 -0.255317351
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.30627187 -0.327981232 -0.334277933 -0.343935613 -0.347029762
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.359161832 -0.359945235 -0.368913567 -0.380235729 -0.398461713
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.399213836 -0.399284019 -0.408989879 -0.428224485 -0.442200811
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.447400078 -0.449261397 -0.454790159 -0.466734078 -0.467614451
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.471618177 -0.473209269 -0.483120435 -0.494906486 -0.496293077
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.563339519 -0.579918045 -0.581015956 -0.60291507 -0.612242656
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.61894364 -0.652729444 -0.731309262 0.117400503 0.12862613
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## 0.447183364 0.510616761 0.519681634 0.627037582 0.788405152
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## 1.035253997 1.041012607 1.118621879 1.397025289 1.453249541
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## 1.463514021 2.829425593 inode3122 inode3123 inode3151
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3159 inode3160 inode3162 inode3217 inode3218
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3219 inode3238 inode3239 inode3241 inode3242
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3246 inode3259 inode3264 inode3269 inode3272
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3274 inode3279 inode3280 inode3282 inode3284
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3288 inode3290 inode3297 inode3301 inode3315
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3316 inode3319 inode3326 inode3351 inode3490
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3495 inode3496 inode3501 inode3502 inode3509
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3513 inode3514 inode3525 inode3538 inode3542
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3572 inode3631 inode3714 inode3732 inode3769
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3970 inode4032 inode4086
## alpha 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103
OUM_BPP<-OUwie(phy = simmap.tre, data = dat, model="OUM", simmap.tree=T,diagn = T)
## Warning: You might not have enough data to fit this model well
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
OUM_BPP
##
## Fit
## lnL AIC AICc BIC model ntax
## 85.24088 -152.4818 -148.196 -134.9206 OUM 52
##
##
## Rates
## 1 2 3 4 5 6
## alpha 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949
## sigma.sq 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326
## 7
## alpha 5.78373949
## sigma.sq 0.02552326
##
## Optima
## 1 2 3 4 5 6
## estimate 0.98278962 1.99999991 3.00016183 3.94380311 4.98768103 6.00000000
## se 0.03331039 0.04697305 0.01001451 0.02575421 0.01410894 0.03321496
## 7
## estimate 6.99998674
## se 0.01485411
##
##
## Half life (another way of reporting alpha)
## 1 2 3 4 5 6 7
## 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441
##
## Arrived at a reliable solution
aic<-setNames(c(BM1_BPP$AICc,OU1_BPP$AICc,OUM_BPP$AICc),
c("BM","OU1","OUM"))
aic
## BM OU1 OUM
## 158.5073 160.7624 -148.1960
aic.w(aic)
## BM OU1 OUM
## 0 0 1
dat<-read.csv("./data/Ouwie_data/LAAO_OUwie_ManyOptions_optima.csv")
BM1_LAAO<-OUwie(phy = simmap.tre,data = dat,model="BM1",simmap.tree=TRUE,diagn = T)
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
BM1_LAAO
##
## Fit
## lnL AIC AICc BIC model ntax
## -77.13118 158.2624 158.5073 162.1649 BM1 52
##
## Rates
## -0.092648244 -0.100295794 -0.128998329 -0.21620634 -0.230245425
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.239964336 -0.257771998 -0.258593859 -0.270929154 -0.291282471
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.318364164 -0.324668291 -0.334277933 -0.337841517 -0.343571052
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.343935613 -0.347029762 -0.348104493 -0.359161832 -0.372459947
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.376103195 -0.378251319 -0.399213836 -0.399284019 -0.402697024
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.404809885 -0.408989879 -0.409571651 -0.410097725 -0.411566673
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.422109758 -0.423308801 -0.423417345 -0.424255936 -0.430927124
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.442200811 -0.454790159 -0.459411318 -0.463327573 -0.463654083
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.478165354 -0.486637693 -0.505966472 -0.539435104 -0.555961591
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.563339519 -0.585142053 -0.612242656 -0.646133988 -0.723025233
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 0.011750916 0.019517693 inode3122 inode3123 inode3151
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3159 inode3160 inode3162 inode3217 inode3218 inode3219
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3238 inode3239 inode3241 inode3242 inode3246 inode3259
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3264 inode3269 inode3272 inode3274 inode3279 inode3280
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3282 inode3284 inode3288 inode3290 inode3297 inode3301
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3315 inode3316 inode3319 inode3326 inode3351 inode3490
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3495 inode3496 inode3501 inode3502 inode3509 inode3513
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3514 inode3525 inode3538 inode3542 inode3572 inode3631
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3714 inode3732 inode3769 inode3970 inode4032 inode4086
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##
## Optima
## -0.092648244 -0.100295794 -0.128998329 -0.21620634 -0.230245425
## estimate 4.0576335 0 0 0 0
## se 0.7261147 0 0 0 0
## -0.239964336 -0.257771998 -0.258593859 -0.270929154 -0.291282471
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.318364164 -0.324668291 -0.334277933 -0.337841517 -0.343571052
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.343935613 -0.347029762 -0.348104493 -0.359161832 -0.372459947
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.376103195 -0.378251319 -0.399213836 -0.399284019 -0.402697024
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.404809885 -0.408989879 -0.409571651 -0.410097725 -0.411566673
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.422109758 -0.423308801 -0.423417345 -0.424255936 -0.430927124
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.442200811 -0.454790159 -0.459411318 -0.463327573 -0.463654083
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.478165354 -0.486637693 -0.505966472 -0.539435104 -0.555961591
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.563339519 -0.585142053 -0.612242656 -0.646133988 -0.723025233
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 0.011750916 0.019517693 inode3122 inode3123 inode3151 inode3159
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 0 0 0 0 0
## se 0 0 0 0 0
##
## Arrived at a reliable solution
OU1_LAAO<-OUwie(phy = simmap.tre, data = dat, model="OU1", simmap.tree=T,diagn = T)
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
OU1_LAAO
##
## Fit
## lnL AIC AICc BIC model ntax
## -77.13118 160.2624 160.7624 166.1161 OU1 52
##
## Rates
## -0.092648244 -0.100295794 -0.128998329 -0.21620634 -0.230245425
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.239964336 -0.257771998 -0.258593859 -0.270929154 -0.291282471
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.318364164 -0.324668291 -0.334277933 -0.337841517 -0.343571052
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.343935613 -0.347029762 -0.348104493 -0.359161832 -0.372459947
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.376103195 -0.378251319 -0.399213836 -0.399284019 -0.402697024
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.404809885 -0.408989879 -0.409571651 -0.410097725 -0.411566673
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.422109758 -0.423308801 -0.423417345 -0.424255936 -0.430927124
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.442200811 -0.454790159 -0.459411318 -0.463327573 -0.463654083
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.478165354 -0.486637693 -0.505966472 -0.539435104 -0.555961591
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.563339519 -0.585142053 -0.612242656 -0.646133988 -0.723025233
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## 0.011750916 0.019517693 inode3122 inode3123 inode3151
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3159 inode3160 inode3162 inode3217 inode3218
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3219 inode3238 inode3239 inode3241 inode3242
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3246 inode3259 inode3264 inode3269 inode3272
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3274 inode3279 inode3280 inode3282 inode3284
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3288 inode3290 inode3297 inode3301 inode3315
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3316 inode3319 inode3326 inode3351 inode3490
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3495 inode3496 inode3501 inode3502 inode3509
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3513 inode3514 inode3525 inode3538 inode3542
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3572 inode3631 inode3714 inode3732 inode3769
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3970 inode4032 inode4086
## alpha 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02
##
##
## Optima
## -0.092648244 -0.100295794 -0.128998329 -0.21620634 -0.230245425
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.239964336 -0.257771998 -0.258593859 -0.270929154 -0.291282471
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.318364164 -0.324668291 -0.334277933 -0.337841517 -0.343571052
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.343935613 -0.347029762 -0.348104493 -0.359161832 -0.372459947
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.376103195 -0.378251319 -0.399213836 -0.399284019 -0.402697024
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.404809885 -0.408989879 -0.409571651 -0.410097725 -0.411566673
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.422109758 -0.423308801 -0.423417345 -0.424255936 -0.430927124
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.442200811 -0.454790159 -0.459411318 -0.463327573 -0.463654083
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.478165354 -0.486637693 -0.505966472 -0.539435104 -0.555961591
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.563339519 -0.585142053 -0.612242656 -0.646133988 -0.723025233
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 0.011750916 0.019517693 inode3122 inode3123 inode3151 inode3159
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##
##
## Half life (another way of reporting alpha)
## -0.092648244 -0.100295794 -0.128998329 -0.21620634 -0.230245425
## 308643937 308643937 308643937 308643937 308643937
## -0.239964336 -0.257771998 -0.258593859 -0.270929154 -0.291282471
## 308643937 308643937 308643937 308643937 308643937
## -0.318364164 -0.324668291 -0.334277933 -0.337841517 -0.343571052
## 308643937 308643937 308643937 308643937 308643937
## -0.343935613 -0.347029762 -0.348104493 -0.359161832 -0.372459947
## 308643937 308643937 308643937 308643937 308643937
## -0.376103195 -0.378251319 -0.399213836 -0.399284019 -0.402697024
## 308643937 308643937 308643937 308643937 308643937
## -0.404809885 -0.408989879 -0.409571651 -0.410097725 -0.411566673
## 308643937 308643937 308643937 308643937 308643937
## -0.422109758 -0.423308801 -0.423417345 -0.424255936 -0.430927124
## 308643937 308643937 308643937 308643937 308643937
## -0.442200811 -0.454790159 -0.459411318 -0.463327573 -0.463654083
## 308643937 308643937 308643937 308643937 308643937
## -0.478165354 -0.486637693 -0.505966472 -0.539435104 -0.555961591
## 308643937 308643937 308643937 308643937 308643937
## -0.563339519 -0.585142053 -0.612242656 -0.646133988 -0.723025233
## 308643937 308643937 308643937 308643937 308643937
## 0.011750916 0.019517693 inode3122 inode3123 inode3151
## 308643937 308643937 308643937 308643937 308643937
## inode3159 inode3160 inode3162 inode3217 inode3218
## 308643937 308643937 308643937 308643937 308643937
## inode3219 inode3238 inode3239 inode3241 inode3242
## 308643937 308643937 308643937 308643937 308643937
## inode3246 inode3259 inode3264 inode3269 inode3272
## 308643937 308643937 308643937 308643937 308643937
## inode3274 inode3279 inode3280 inode3282 inode3284
## 308643937 308643937 308643937 308643937 308643937
## inode3288 inode3290 inode3297 inode3301 inode3315
## 308643937 308643937 308643937 308643937 308643937
## inode3316 inode3319 inode3326 inode3351 inode3490
## 308643937 308643937 308643937 308643937 308643937
## inode3495 inode3496 inode3501 inode3502 inode3509
## 308643937 308643937 308643937 308643937 308643937
## inode3513 inode3514 inode3525 inode3538 inode3542
## 308643937 308643937 308643937 308643937 308643937
## inode3572 inode3631 inode3714 inode3732 inode3769
## 308643937 308643937 308643937 308643937 308643937
## inode3970 inode4032 inode4086
## 308643937 308643937 308643937
##
## Arrived at a reliable solution
OU1_LAAO$eigval
## [1] 2.6e+01 1.3e-06
OU1_LAAO$solution.se
## -0.092648244 -0.100295794 -0.128998329 -0.21620634 -0.230245425
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.239964336 -0.257771998 -0.258593859 -0.270929154 -0.291282471
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.318364164 -0.324668291 -0.334277933 -0.337841517 -0.343571052
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.343935613 -0.347029762 -0.348104493 -0.359161832 -0.372459947
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.376103195 -0.378251319 -0.399213836 -0.399284019 -0.402697024
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.404809885 -0.408989879 -0.409571651 -0.410097725 -0.411566673
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.422109758 -0.423308801 -0.423417345 -0.424255936 -0.430927124
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.442200811 -0.454790159 -0.459411318 -0.463327573 -0.463654083
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.478165354 -0.486637693 -0.505966472 -0.539435104 -0.555961591
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.563339519 -0.585142053 -0.612242656 -0.646133988 -0.723025233
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## 0.011750916 0.019517693 inode3122 inode3123 inode3151
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3159 inode3160 inode3162 inode3217 inode3218
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3219 inode3238 inode3239 inode3241 inode3242
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3246 inode3259 inode3264 inode3269 inode3272
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3274 inode3279 inode3280 inode3282 inode3284
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3288 inode3290 inode3297 inode3301 inode3315
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3316 inode3319 inode3326 inode3351 inode3490
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3495 inode3496 inode3501 inode3502 inode3509
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3513 inode3514 inode3525 inode3538 inode3542
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3572 inode3631 inode3714 inode3732 inode3769
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3970 inode4032 inode4086
## alpha 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103
OUM_LAAO<-OUwie(phy = simmap.tre, data = dat, model="OUM", simmap.tree=T,diagn = T)
## Warning: You might not have enough data to fit this model well
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
OUM_LAAO
##
## Fit
## lnL AIC AICc BIC model ntax
## 85.24088 -152.4818 -148.196 -134.9206 OUM 52
##
##
## Rates
## 1 2 3 4 5 6
## alpha 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949
## sigma.sq 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326
## 7
## alpha 5.78373949
## sigma.sq 0.02552326
##
## Optima
## 1 2 3 4 5 6
## estimate 0.98278962 1.99999991 3.00016183 3.94380311 4.98768103 6.00000000
## se 0.03331039 0.04697305 0.01001451 0.02575421 0.01410894 0.03321496
## 7
## estimate 6.99998674
## se 0.01485411
##
##
## Half life (another way of reporting alpha)
## 1 2 3 4 5 6 7
## 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441
##
## Arrived at a reliable solution
aic<-setNames(c(BM1_LAAO$AICc,OU1_LAAO$AICc,OUM_LAAO$AICc),
c("BM","OU1","OUM"))
aic
## BM OU1 OUM
## 158.5073 160.7624 -148.1960
aic.w(aic)
## BM OU1 OUM
## 0 0 1
dat<-read.csv("./data/Ouwie_data/KSPI_OUwie_ManyOptions_optima.csv")
BM1_KSPI<-OUwie(phy = simmap.tre,data = dat,model="BM1",simmap.tree=TRUE,diagn = T)
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
BM1_KSPI
##
## Fit
## lnL AIC AICc BIC model ntax
## -77.13118 158.2624 158.5073 162.1649 BM1 52
##
## Rates
## -0.115762862 -0.218459259 -0.276269351 -0.324668291 -0.334277933
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.343935613 -0.347029762 -0.36429282 -0.36971411 -0.376347838
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.395173036 -0.399213836 -0.399284019 -0.40249729 -0.419749836
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.422992017 -0.449261397 -0.451042648 -0.454790159 -0.4580531
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.458694297 -0.461032003 -0.466734078 -0.478411682 -0.494906486
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.496224454 -0.507701406 -0.52278517 -0.527324428 -0.527913521
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.535408592 -0.539435104 -0.548287973 -0.555961591 -0.569277353
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.580540919 -0.581015956 -0.600904674 -0.651365854 -0.665162495
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.684832772 -0.69527236 -0.709372748 -0.731309262 -0.779848299
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.825512855 -0.874226881 -0.96572225 0.042118192 0.173328997
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 0.867471889 2.30436465 inode3122 inode3123 inode3151
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3159 inode3160 inode3162 inode3217 inode3218 inode3219
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3238 inode3239 inode3241 inode3242 inode3246 inode3259
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3264 inode3269 inode3272 inode3274 inode3279 inode3280
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3282 inode3284 inode3288 inode3290 inode3297 inode3301
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3315 inode3316 inode3319 inode3326 inode3351 inode3490
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3495 inode3496 inode3501 inode3502 inode3509 inode3513
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3514 inode3525 inode3538 inode3542 inode3572 inode3631
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3714 inode3732 inode3769 inode3970 inode4032 inode4086
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##
## Optima
## -0.115762862 -0.218459259 -0.276269351 -0.324668291 -0.334277933
## estimate 4.0576335 0 0 0 0
## se 0.7261147 0 0 0 0
## -0.343935613 -0.347029762 -0.36429282 -0.36971411 -0.376347838
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.395173036 -0.399213836 -0.399284019 -0.40249729 -0.419749836
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.422992017 -0.449261397 -0.451042648 -0.454790159 -0.4580531
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.458694297 -0.461032003 -0.466734078 -0.478411682 -0.494906486
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.496224454 -0.507701406 -0.52278517 -0.527324428 -0.527913521
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.535408592 -0.539435104 -0.548287973 -0.555961591 -0.569277353
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.580540919 -0.581015956 -0.600904674 -0.651365854 -0.665162495
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.684832772 -0.69527236 -0.709372748 -0.731309262 -0.779848299
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.825512855 -0.874226881 -0.96572225 0.042118192 0.173328997
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 0.867471889 2.30436465 inode3122 inode3123 inode3151 inode3159
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 0 0 0 0 0
## se 0 0 0 0 0
##
## Arrived at a reliable solution
OU1_KSPI<-OUwie(phy = simmap.tre, data = dat, model="OU1", simmap.tree=T,diagn = T)
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
OU1_KSPI
##
## Fit
## lnL AIC AICc BIC model ntax
## -77.13118 160.2624 160.7624 166.1161 OU1 52
##
## Rates
## -0.115762862 -0.218459259 -0.276269351 -0.324668291 -0.334277933
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.343935613 -0.347029762 -0.36429282 -0.36971411 -0.376347838
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.395173036 -0.399213836 -0.399284019 -0.40249729 -0.419749836
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.422992017 -0.449261397 -0.451042648 -0.454790159 -0.4580531
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.458694297 -0.461032003 -0.466734078 -0.478411682 -0.494906486
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.496224454 -0.507701406 -0.52278517 -0.527324428 -0.527913521
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.535408592 -0.539435104 -0.548287973 -0.555961591 -0.569277353
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.580540919 -0.581015956 -0.600904674 -0.651365854 -0.665162495
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.684832772 -0.69527236 -0.709372748 -0.731309262 -0.779848299
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.825512855 -0.874226881 -0.96572225 0.042118192 0.173328997
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## 0.867471889 2.30436465 inode3122 inode3123 inode3151
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3159 inode3160 inode3162 inode3217 inode3218
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3219 inode3238 inode3239 inode3241 inode3242
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3246 inode3259 inode3264 inode3269 inode3272
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3274 inode3279 inode3280 inode3282 inode3284
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3288 inode3290 inode3297 inode3301 inode3315
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3316 inode3319 inode3326 inode3351 inode3490
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3495 inode3496 inode3501 inode3502 inode3509
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3513 inode3514 inode3525 inode3538 inode3542
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3572 inode3631 inode3714 inode3732 inode3769
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3970 inode4032 inode4086
## alpha 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02
##
##
## Optima
## -0.115762862 -0.218459259 -0.276269351 -0.324668291 -0.334277933
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.343935613 -0.347029762 -0.36429282 -0.36971411 -0.376347838
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.395173036 -0.399213836 -0.399284019 -0.40249729 -0.419749836
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.422992017 -0.449261397 -0.451042648 -0.454790159 -0.4580531
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.458694297 -0.461032003 -0.466734078 -0.478411682 -0.494906486
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.496224454 -0.507701406 -0.52278517 -0.527324428 -0.527913521
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.535408592 -0.539435104 -0.548287973 -0.555961591 -0.569277353
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.580540919 -0.581015956 -0.600904674 -0.651365854 -0.665162495
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.684832772 -0.69527236 -0.709372748 -0.731309262 -0.779848299
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.825512855 -0.874226881 -0.96572225 0.042118192 0.173328997
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 0.867471889 2.30436465 inode3122 inode3123 inode3151 inode3159
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##
##
## Half life (another way of reporting alpha)
## -0.115762862 -0.218459259 -0.276269351 -0.324668291 -0.334277933
## 308643937 308643937 308643937 308643937 308643937
## -0.343935613 -0.347029762 -0.36429282 -0.36971411 -0.376347838
## 308643937 308643937 308643937 308643937 308643937
## -0.395173036 -0.399213836 -0.399284019 -0.40249729 -0.419749836
## 308643937 308643937 308643937 308643937 308643937
## -0.422992017 -0.449261397 -0.451042648 -0.454790159 -0.4580531
## 308643937 308643937 308643937 308643937 308643937
## -0.458694297 -0.461032003 -0.466734078 -0.478411682 -0.494906486
## 308643937 308643937 308643937 308643937 308643937
## -0.496224454 -0.507701406 -0.52278517 -0.527324428 -0.527913521
## 308643937 308643937 308643937 308643937 308643937
## -0.535408592 -0.539435104 -0.548287973 -0.555961591 -0.569277353
## 308643937 308643937 308643937 308643937 308643937
## -0.580540919 -0.581015956 -0.600904674 -0.651365854 -0.665162495
## 308643937 308643937 308643937 308643937 308643937
## -0.684832772 -0.69527236 -0.709372748 -0.731309262 -0.779848299
## 308643937 308643937 308643937 308643937 308643937
## -0.825512855 -0.874226881 -0.96572225 0.042118192 0.173328997
## 308643937 308643937 308643937 308643937 308643937
## 0.867471889 2.30436465 inode3122 inode3123 inode3151
## 308643937 308643937 308643937 308643937 308643937
## inode3159 inode3160 inode3162 inode3217 inode3218
## 308643937 308643937 308643937 308643937 308643937
## inode3219 inode3238 inode3239 inode3241 inode3242
## 308643937 308643937 308643937 308643937 308643937
## inode3246 inode3259 inode3264 inode3269 inode3272
## 308643937 308643937 308643937 308643937 308643937
## inode3274 inode3279 inode3280 inode3282 inode3284
## 308643937 308643937 308643937 308643937 308643937
## inode3288 inode3290 inode3297 inode3301 inode3315
## 308643937 308643937 308643937 308643937 308643937
## inode3316 inode3319 inode3326 inode3351 inode3490
## 308643937 308643937 308643937 308643937 308643937
## inode3495 inode3496 inode3501 inode3502 inode3509
## 308643937 308643937 308643937 308643937 308643937
## inode3513 inode3514 inode3525 inode3538 inode3542
## 308643937 308643937 308643937 308643937 308643937
## inode3572 inode3631 inode3714 inode3732 inode3769
## 308643937 308643937 308643937 308643937 308643937
## inode3970 inode4032 inode4086
## 308643937 308643937 308643937
##
## Arrived at a reliable solution
OU1_KSPI$eigval
## [1] 2.6e+01 1.3e-06
OU1_KSPI$solution.se
## -0.115762862 -0.218459259 -0.276269351 -0.324668291 -0.334277933
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.343935613 -0.347029762 -0.36429282 -0.36971411 -0.376347838
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.395173036 -0.399213836 -0.399284019 -0.40249729 -0.419749836
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.422992017 -0.449261397 -0.451042648 -0.454790159 -0.4580531
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.458694297 -0.461032003 -0.466734078 -0.478411682 -0.494906486
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.496224454 -0.507701406 -0.52278517 -0.527324428 -0.527913521
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.535408592 -0.539435104 -0.548287973 -0.555961591 -0.569277353
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.580540919 -0.581015956 -0.600904674 -0.651365854 -0.665162495
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.684832772 -0.69527236 -0.709372748 -0.731309262 -0.779848299
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.825512855 -0.874226881 -0.96572225 0.042118192 0.173328997
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## 0.867471889 2.30436465 inode3122 inode3123 inode3151
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3159 inode3160 inode3162 inode3217 inode3218
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3219 inode3238 inode3239 inode3241 inode3242
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3246 inode3259 inode3264 inode3269 inode3272
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3274 inode3279 inode3280 inode3282 inode3284
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3288 inode3290 inode3297 inode3301 inode3315
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3316 inode3319 inode3326 inode3351 inode3490
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3495 inode3496 inode3501 inode3502 inode3509
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3513 inode3514 inode3525 inode3538 inode3542
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3572 inode3631 inode3714 inode3732 inode3769
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3970 inode4032 inode4086
## alpha 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103
OUM_KSPI<-OUwie(phy = simmap.tre, data = dat, model="OUM", simmap.tree=T,diagn = T)
## Warning: You might not have enough data to fit this model well
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
OUM_KSPI
##
## Fit
## lnL AIC AICc BIC model ntax
## 85.24088 -152.4818 -148.196 -134.9206 OUM 52
##
##
## Rates
## 1 2 3 4 5 6
## alpha 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949
## sigma.sq 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326
## 7
## alpha 5.78373949
## sigma.sq 0.02552326
##
## Optima
## 1 2 3 4 5 6
## estimate 0.98278962 1.99999991 3.00016183 3.94380311 4.98768103 6.00000000
## se 0.03331039 0.04697305 0.01001451 0.02575421 0.01410894 0.03321496
## 7
## estimate 6.99998674
## se 0.01485411
##
##
## Half life (another way of reporting alpha)
## 1 2 3 4 5 6 7
## 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441
##
## Arrived at a reliable solution
aic<-setNames(c(BM1_KSPI$AICc,OU1_KSPI$AICc,OUM_KSPI$AICc),
c("BM","OU1","OUM"))
aic
## BM OU1 OUM
## 158.5073 160.7624 -148.1960
aic.w(aic)
## BM OU1 OUM
## 0 0 1
dat<-read.csv("./data/Ouwie_data/GF_OUwie_ManyOptions_optima.csv")
BM1_GF<-OUwie(phy = simmap.tre,data = dat,model="BM1",simmap.tree=TRUE,diagn = T)
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
BM1_GF
##
## Fit
## lnL AIC AICc BIC model ntax
## -77.13118 158.2624 158.5073 162.1649 BM1 52
##
## Rates
## -0.101480746 -0.199120618 -0.208294348 -0.223619452 -0.282532123
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.282712808 -0.310359147 -0.310940604 -0.324668291 -0.325799169
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.339426699 -0.347029762 -0.359161832 -0.368572056 -0.384774302
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.389184624 -0.396332642 -0.399213836 -0.399284019 -0.404661486
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.409662437 -0.419808798 -0.423308801 -0.425565648 -0.42583897
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.438880858 -0.448896787 -0.454790159 -0.45813357 -0.460589809
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.462169254 -0.462264075 -0.463092209 -0.473210272 -0.481264314
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.491651278 -0.535408592 -0.539435104 -0.546444401 -0.555961591
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.562419106 -0.575631106 -0.601151125 -0.603132172 -0.609558762
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## -0.612242656 -0.651847915 -0.654661809 -0.681722879 -0.900691872
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## 0.079914355 1.349473949 inode3122 inode3123 inode3151
## alpha NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3159 inode3160 inode3162 inode3217 inode3218 inode3219
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3238 inode3239 inode3241 inode3242 inode3246 inode3259
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3264 inode3269 inode3272 inode3274 inode3279 inode3280
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3282 inode3284 inode3288 inode3290 inode3297 inode3301
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3315 inode3316 inode3319 inode3326 inode3351 inode3490
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3495 inode3496 inode3501 inode3502 inode3509 inode3513
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3514 inode3525 inode3538 inode3542 inode3572 inode3631
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
## inode3714 inode3732 inode3769 inode3970 inode4032 inode4086
## alpha NA NA NA NA NA NA
## sigma.sq 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937 0.04805937
##
## Optima
## -0.101480746 -0.199120618 -0.208294348 -0.223619452 -0.282532123
## estimate 4.0576335 0 0 0 0
## se 0.7261147 0 0 0 0
## -0.282712808 -0.310359147 -0.310940604 -0.324668291 -0.325799169
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.339426699 -0.347029762 -0.359161832 -0.368572056 -0.384774302
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.389184624 -0.396332642 -0.399213836 -0.399284019 -0.404661486
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.409662437 -0.419808798 -0.423308801 -0.425565648 -0.42583897
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.438880858 -0.448896787 -0.454790159 -0.45813357 -0.460589809
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.462169254 -0.462264075 -0.463092209 -0.473210272 -0.481264314
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.491651278 -0.535408592 -0.539435104 -0.546444401 -0.555961591
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.562419106 -0.575631106 -0.601151125 -0.603132172 -0.609558762
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## -0.612242656 -0.651847915 -0.654661809 -0.681722879 -0.900691872
## estimate 0 0 0 0 0
## se 0 0 0 0 0
## 0.079914355 1.349473949 inode3122 inode3123 inode3151 inode3159
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 0 0 0 0 0 0
## se 0 0 0 0 0 0
## inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 0 0 0 0 0
## se 0 0 0 0 0
##
## Arrived at a reliable solution
OU1_GF<-OUwie(phy = simmap.tre, data = dat, model="OU1", simmap.tree=T,diagn = T)
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
OU1_GF
##
## Fit
## lnL AIC AICc BIC model ntax
## -77.13118 160.2624 160.7624 166.1161 OU1 52
##
## Rates
## -0.101480746 -0.199120618 -0.208294348 -0.223619452 -0.282532123
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.282712808 -0.310359147 -0.310940604 -0.324668291 -0.325799169
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.339426699 -0.347029762 -0.359161832 -0.368572056 -0.384774302
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.389184624 -0.396332642 -0.399213836 -0.399284019 -0.404661486
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.409662437 -0.419808798 -0.423308801 -0.425565648 -0.42583897
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.438880858 -0.448896787 -0.454790159 -0.45813357 -0.460589809
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.462169254 -0.462264075 -0.463092209 -0.473210272 -0.481264314
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.491651278 -0.535408592 -0.539435104 -0.546444401 -0.555961591
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.562419106 -0.575631106 -0.601151125 -0.603132172 -0.609558762
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## -0.612242656 -0.651847915 -0.654661809 -0.681722879 -0.900691872
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## 0.079914355 1.349473949 inode3122 inode3123 inode3151
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3159 inode3160 inode3162 inode3217 inode3218
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3219 inode3238 inode3239 inode3241 inode3242
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3246 inode3259 inode3264 inode3269 inode3272
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3274 inode3279 inode3280 inode3282 inode3284
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3288 inode3290 inode3297 inode3301 inode3315
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3316 inode3319 inode3326 inode3351 inode3490
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3495 inode3496 inode3501 inode3502 inode3509
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3513 inode3514 inode3525 inode3538 inode3542
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3572 inode3631 inode3714 inode3732 inode3769
## alpha 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02 4.805130e-02
## inode3970 inode4032 inode4086
## alpha 2.245783e-09 2.245783e-09 2.245783e-09
## sigma.sq 4.805130e-02 4.805130e-02 4.805130e-02
##
##
## Optima
## -0.101480746 -0.199120618 -0.208294348 -0.223619452 -0.282532123
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.282712808 -0.310359147 -0.310940604 -0.324668291 -0.325799169
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.339426699 -0.347029762 -0.359161832 -0.368572056 -0.384774302
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.389184624 -0.396332642 -0.399213836 -0.399284019 -0.404661486
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.409662437 -0.419808798 -0.423308801 -0.425565648 -0.42583897
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.438880858 -0.448896787 -0.454790159 -0.45813357 -0.460589809
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.462169254 -0.462264075 -0.463092209 -0.473210272 -0.481264314
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.491651278 -0.535408592 -0.539435104 -0.546444401 -0.555961591
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.562419106 -0.575631106 -0.601151125 -0.603132172 -0.609558762
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## -0.612242656 -0.651847915 -0.654661809 -0.681722879 -0.900691872
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## 0.079914355 1.349473949 inode3122 inode3123 inode3151 inode3159
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3160 inode3162 inode3217 inode3218 inode3219 inode3238
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3239 inode3241 inode3242 inode3246 inode3259 inode3264
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3269 inode3272 inode3274 inode3279 inode3280 inode3282
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3284 inode3288 inode3290 inode3297 inode3301 inode3315
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3316 inode3319 inode3326 inode3351 inode3490 inode3495
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3496 inode3501 inode3502 inode3509 inode3513 inode3514
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3525 inode3538 inode3542 inode3572 inode3631 inode3714
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
## inode3732 inode3769 inode3970 inode4032 inode4086
## estimate 4.0576335 4.0576335 4.0576335 4.0576335 4.0576335
## se 0.7260536 0.7260536 0.7260536 0.7260536 0.7260536
##
##
## Half life (another way of reporting alpha)
## -0.101480746 -0.199120618 -0.208294348 -0.223619452 -0.282532123
## 308643937 308643937 308643937 308643937 308643937
## -0.282712808 -0.310359147 -0.310940604 -0.324668291 -0.325799169
## 308643937 308643937 308643937 308643937 308643937
## -0.339426699 -0.347029762 -0.359161832 -0.368572056 -0.384774302
## 308643937 308643937 308643937 308643937 308643937
## -0.389184624 -0.396332642 -0.399213836 -0.399284019 -0.404661486
## 308643937 308643937 308643937 308643937 308643937
## -0.409662437 -0.419808798 -0.423308801 -0.425565648 -0.42583897
## 308643937 308643937 308643937 308643937 308643937
## -0.438880858 -0.448896787 -0.454790159 -0.45813357 -0.460589809
## 308643937 308643937 308643937 308643937 308643937
## -0.462169254 -0.462264075 -0.463092209 -0.473210272 -0.481264314
## 308643937 308643937 308643937 308643937 308643937
## -0.491651278 -0.535408592 -0.539435104 -0.546444401 -0.555961591
## 308643937 308643937 308643937 308643937 308643937
## -0.562419106 -0.575631106 -0.601151125 -0.603132172 -0.609558762
## 308643937 308643937 308643937 308643937 308643937
## -0.612242656 -0.651847915 -0.654661809 -0.681722879 -0.900691872
## 308643937 308643937 308643937 308643937 308643937
## 0.079914355 1.349473949 inode3122 inode3123 inode3151
## 308643937 308643937 308643937 308643937 308643937
## inode3159 inode3160 inode3162 inode3217 inode3218
## 308643937 308643937 308643937 308643937 308643937
## inode3219 inode3238 inode3239 inode3241 inode3242
## 308643937 308643937 308643937 308643937 308643937
## inode3246 inode3259 inode3264 inode3269 inode3272
## 308643937 308643937 308643937 308643937 308643937
## inode3274 inode3279 inode3280 inode3282 inode3284
## 308643937 308643937 308643937 308643937 308643937
## inode3288 inode3290 inode3297 inode3301 inode3315
## 308643937 308643937 308643937 308643937 308643937
## inode3316 inode3319 inode3326 inode3351 inode3490
## 308643937 308643937 308643937 308643937 308643937
## inode3495 inode3496 inode3501 inode3502 inode3509
## 308643937 308643937 308643937 308643937 308643937
## inode3513 inode3514 inode3525 inode3538 inode3542
## 308643937 308643937 308643937 308643937 308643937
## inode3572 inode3631 inode3714 inode3732 inode3769
## 308643937 308643937 308643937 308643937 308643937
## inode3970 inode4032 inode4086
## 308643937 308643937 308643937
##
## Arrived at a reliable solution
OU1_GF$eigval
## [1] 2.6e+01 1.3e-06
OU1_GF$solution.se
## -0.101480746 -0.199120618 -0.208294348 -0.223619452 -0.282532123
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.282712808 -0.310359147 -0.310940604 -0.324668291 -0.325799169
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.339426699 -0.347029762 -0.359161832 -0.368572056 -0.384774302
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.389184624 -0.396332642 -0.399213836 -0.399284019 -0.404661486
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.409662437 -0.419808798 -0.423308801 -0.425565648 -0.42583897
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.438880858 -0.448896787 -0.454790159 -0.45813357 -0.460589809
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.462169254 -0.462264075 -0.463092209 -0.473210272 -0.481264314
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.491651278 -0.535408592 -0.539435104 -0.546444401 -0.555961591
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.562419106 -0.575631106 -0.601151125 -0.603132172 -0.609558762
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## -0.612242656 -0.651847915 -0.654661809 -0.681722879 -0.900691872
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## 0.079914355 1.349473949 inode3122 inode3123 inode3151
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3159 inode3160 inode3162 inode3217 inode3218
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3219 inode3238 inode3239 inode3241 inode3242
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3246 inode3259 inode3264 inode3269 inode3272
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3274 inode3279 inode3280 inode3282 inode3284
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3288 inode3290 inode3297 inode3301 inode3315
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3316 inode3319 inode3326 inode3351 inode3490
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3495 inode3496 inode3501 inode3502 inode3509
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3513 inode3514 inode3525 inode3538 inode3542
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3572 inode3631 inode3714 inode3732 inode3769
## alpha 882.7127566 882.7127566 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103 0.1961103 0.1961103
## inode3970 inode4032 inode4086
## alpha 882.7127566 882.7127566 882.7127566
## sigma.sq 0.1961103 0.1961103 0.1961103
OUM_GF<-OUwie(phy = simmap.tre, data = dat, model="OUM", simmap.tree=T,diagn = T)
## Warning: You might not have enough data to fit this model well
## Initializing...
## Finished. Begin thorough search...
## Finished. Summarizing results.
OUM_GF
##
## Fit
## lnL AIC AICc BIC model ntax
## 85.24088 -152.4818 -148.196 -134.9206 OUM 52
##
##
## Rates
## 1 2 3 4 5 6
## alpha 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949 5.78373949
## sigma.sq 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326 0.02552326
## 7
## alpha 5.78373949
## sigma.sq 0.02552326
##
## Optima
## 1 2 3 4 5 6
## estimate 0.98278962 1.99999991 3.00016183 3.94380311 4.98768103 6.00000000
## se 0.03331039 0.04697305 0.01001451 0.02575421 0.01410894 0.03321496
## 7
## estimate 6.99998674
## se 0.01485411
##
##
## Half life (another way of reporting alpha)
## 1 2 3 4 5 6 7
## 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441 0.1198441
##
## Arrived at a reliable solution
aic<-setNames(c(BM1_GF$AICc,OU1_GF$AICc,OUM_GF$AICc),
c("BM","OU1","OUM"))
aic
## BM OU1 OUM
## 158.5073 160.7624 -148.1960
aic.w(aic)
## BM OU1 OUM
## 0 0 1
devtools::session_info()
## ─ Session info ──────────────────────────────────────────────────────────
## setting value
## version R version 3.5.2 (2018-12-20)
## os macOS Mojave 10.14.6
## system x86_64, darwin15.6.0
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Asia/Tokyo
## date 2019-10-17
##
## ─ Packages ──────────────────────────────────────────────────────────────
## package * version date lib
## animation 2.6 2018-12-11 [1]
## ape * 5.3 2019-03-17 [1]
## assertthat 0.2.1 2019-03-21 [1]
## backports 1.1.4 2019-04-10 [1]
## BAMMtools * 2.1.6 2017-02-03 [1]
## bitops 1.0-6 2013-08-17 [1]
## broom 0.5.2 2019-04-07 [1]
## callr 3.2.0 2019-03-15 [1]
## captioner * 2.2.3 2015-07-16 [1]
## caTools 1.17.1.2 2019-03-06 [1]
## cellranger 1.1.0 2016-07-27 [1]
## cli 1.1.0 2019-03-19 [1]
## clusterGeneration 1.3.4 2015-02-18 [1]
## coda * 0.19-2 2018-10-08 [1]
## codetools 0.2-16 2018-12-24 [1]
## colorspace 1.4-1 2019-03-18 [1]
## combinat 0.0-8 2012-10-29 [1]
## corHMM 1.22 2017-07-19 [1]
## corpcor 1.6.9 2017-04-01 [1]
## crayon 1.3.4 2017-09-16 [1]
## desc 1.2.0 2018-05-01 [1]
## deSolve 1.21 2018-05-09 [1]
## devtools 2.0.2 2019-04-08 [1]
## digest 0.6.19 2019-05-20 [1]
## dplyr * 0.8.1 2019-05-14 [1]
## evaluate 0.14 2019-05-28 [1]
## expm 0.999-4 2019-03-21 [1]
## fastmatch 1.1-0 2017-01-28 [1]
## forcats * 0.4.0 2019-02-17 [1]
## fs 1.3.1 2019-05-06 [1]
## gdata 2.18.0 2017-06-06 [1]
## geiger * 2.0.6.1 2019-01-16 [1]
## generics 0.0.2 2018-11-29 [1]
## GenSA 1.1.7 2018-01-17 [1]
## ggplot2 * 3.1.1 2019-04-07 [1]
## glue 1.3.1 2019-03-12 [1]
## gmp 0.5-13.5 2019-03-11 [1]
## gplots 3.0.1.1 2019-01-27 [1]
## gtable 0.3.0 2019-03-25 [1]
## gtools 3.8.1 2018-06-26 [1]
## haven 2.1.0 2019-02-19 [1]
## hms 0.4.2 2018-03-10 [1]
## htmltools 0.3.6 2017-04-28 [1]
## httr 1.4.0 2018-12-11 [1]
## igraph 1.2.4.1 2019-04-22 [1]
## jsonlite 1.6 2018-12-07 [1]
## kableExtra * 1.1.0 2019-03-16 [1]
## KernSmooth 2.23-15 2015-06-29 [1]
## knitr 1.23 2019-05-18 [1]
## lattice * 0.20-38 2018-11-04 [1]
## lazyeval 0.2.2 2019-03-15 [1]
## lubridate 1.7.4 2018-04-11 [1]
## magrittr 1.5 2014-11-22 [1]
## maps * 3.3.0 2018-04-03 [1]
## MASS 7.3-51.4 2019-03-31 [1]
## Matrix 1.2-17 2019-03-22 [1]
## memoise 1.1.0 2017-04-21 [1]
## mnormt 1.5-5 2016-10-15 [1]
## modelr 0.1.4 2019-02-18 [1]
## munsell 0.5.0 2018-06-12 [1]
## mvtnorm 1.0-10 2019-03-05 [1]
## nlme 3.1-140 2019-05-12 [1]
## nloptr * 1.2.1 2018-10-03 [1]
## nnet 7.3-12 2016-02-02 [1]
## numDeriv 2016.8-1 2016-08-27 [1]
## OUwie * 1.53 2019-06-11 [1]
## paleotree 3.3.0 2019-06-04 [1]
## phangorn 2.5.3 2019-03-23 [1]
## phytools * 0.6-60 2018-09-28 [1]
## pillar 1.4.1 2019-05-28 [1]
## pkgbuild 1.0.3 2019-03-20 [1]
## pkgconfig 2.0.2 2018-08-16 [1]
## pkgload 1.0.2 2018-10-29 [1]
## plotrix 3.7-5 2019-04-07 [1]
## plyr 1.8.4 2016-06-08 [1]
## png 0.1-7 2013-12-03 [1]
## prettyunits 1.0.2 2015-07-13 [1]
## processx 3.3.1 2019-05-08 [1]
## ps 1.3.0 2018-12-21 [1]
## purrr * 0.3.2 2019-03-15 [1]
## quadprog 1.5-7 2019-05-06 [1]
## R6 2.4.0 2019-02-14 [1]
## Rcpp 1.0.1 2019-03-17 [1]
## RCurl 1.95-4.12 2019-03-04 [1]
## readr * 1.3.1 2018-12-21 [1]
## readxl 1.3.1 2019-03-13 [1]
## remotes 2.0.4 2019-04-10 [1]
## reshape2 * 1.4.3 2017-12-11 [1]
## rlang 0.3.4 2019-04-07 [1]
## rmarkdown 1.13 2019-05-22 [1]
## Rmpfr 0.7-2 2019-01-22 [1]
## rprojroot 1.3-2 2018-01-03 [1]
## rstudioapi 0.10 2019-03-19 [1]
## rvest 0.3.4 2019-05-15 [1]
## scales 1.0.0 2018-08-09 [1]
## scatterplot3d 0.3-41 2018-03-14 [1]
## sessioninfo 1.1.1 2018-11-05 [1]
## spptest * 0.4 2019-07-10 [1]
## stringi 1.4.3 2019-03-12 [1]
## stringr * 1.4.0 2019-02-10 [1]
## subplex 1.5-4 2018-04-05 [1]
## testthat 2.1.1 2019-04-23 [1]
## tibble * 2.1.1 2019-03-16 [1]
## tidyr * 0.8.3 2019-03-01 [1]
## tidyselect 0.2.5 2018-10-11 [1]
## tidyverse * 1.2.1 2017-11-14 [1]
## usethis 1.5.0 2019-04-07 [1]
## viridisLite 0.3.0 2018-02-01 [1]
## webshot 0.5.1 2018-09-28 [1]
## withr 2.1.2 2018-03-15 [1]
## xfun 0.7 2019-05-14 [1]
## xml2 1.2.0 2018-01-24 [1]
## yaml 2.2.0 2018-07-25 [1]
## source
## CRAN (R 3.5.0)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.0)
## CRAN (R 3.5.0)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.0)
## CRAN (R 3.5.2)
## CRAN (R 3.5.0)
## CRAN (R 3.5.2)
## CRAN (R 3.5.0)
## CRAN (R 3.5.0)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.0)
## CRAN (R 3.5.0)
## CRAN (R 3.5.0)
## CRAN (R 3.5.0)
## CRAN (R 3.5.0)
## CRAN (R 3.5.0)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.0)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.0)
## CRAN (R 3.5.2)
## CRAN (R 3.5.0)
## CRAN (R 3.5.0)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.0)
## CRAN (R 3.5.2)
## CRAN (R 3.5.0)
## CRAN (R 3.5.0)
## CRAN (R 3.5.0)
## CRAN (R 3.5.2)
## CRAN (R 3.5.0)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.0)
## CRAN (R 3.5.0)
## CRAN (R 3.5.0)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.0)
## CRAN (R 3.5.0)
## CRAN (R 3.5.2)
## CRAN (R 3.5.0)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.0)
## CRAN (R 3.5.2)
## CRAN (R 3.5.0)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.0)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.0)
## CRAN (R 3.5.0)
## CRAN (R 3.5.2)
## CRAN (R 3.5.0)
## CRAN (R 3.5.0)
## CRAN (R 3.5.0)
## CRAN (R 3.5.2)
## CRAN (R 3.5.0)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.0)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.0)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.0)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.0)
## CRAN (R 3.5.0)
## CRAN (R 3.5.0)
## Github (myllym/spptest@58962f7)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.0)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.2)
## CRAN (R 3.5.0)
## CRAN (R 3.5.0)
## CRAN (R 3.5.2)
## CRAN (R 3.5.0)
## CRAN (R 3.5.0)
## CRAN (R 3.5.0)
## CRAN (R 3.5.2)
## CRAN (R 3.5.0)
## CRAN (R 3.5.0)
##
## [1] /Library/Frameworks/R.framework/Versions/3.5/Resources/library